Search results

• MetaCompare
  MetaCompare is a computational pipeline for prioritizing resistome risk by estimating the potential for ARGs to be ...., Heath, L. S., Xia, K., & Zhang, L. (2018). MetaCompare: A computational pipeline for prioritizing environmental resistome risk. FEMS microbiology ecology.]
  3 KB (304 words) - 21:21, 6 December 2019
• Pipits
  PIPITS is an automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences from the ...S. Read, Robert I. Griffiths and Karsten Schonrogge, PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illum
  3 KB (299 words) - 17:06, 10 June 2022
• MIDAS
  MIDAS is an integrated pipeline that leverages >30,000 reference genomes to estimate bacterial species abun ...B Rodriguez-Mueller, N Garud, and KS Pollard. "An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biog
  3 KB (305 words) - 17:23, 10 June 2022
• Redundans
  Redundans pipeline assists an assembly of heterozygous genomes. .../2457531 Leszek P. Pryszcz and Toni Gabaldón (2016) Redundans: an assembly pipeline for highly heterozygous genomes. NAR. doi: 10.1093/nar/gkw294]
  3 KB (332 words) - 21:24, 6 December 2019
• HiC-Pro
  [[Category:Software]][[Category:Biology]][[Category:Pipeline]][[Category:Genomics]] The pipeline is flexible, scalable and optimized. It can operate either on a single lapt
  3 KB (432 words) - 18:17, 15 August 2022
• RGAugury
  A pipeline consisted of a couple of scripts for genome-wide RGAs prediction, most of s ...Quan, X., Jia, G., Xiao, J., Cloutier, S. and You, F.M. (2016) RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants. BMC
  3 KB (354 words) - 21:29, 30 November 2023
• PhyloPhlAn2
  ...can specify the preferred software to be used to perform each step of the pipeline. In addition, several parameters can be used to define whether to apply tri
  3 KB (375 words) - 17:57, 9 June 2022
• Juicer
  ...and command line tools for feature annotation on the Hi-C maps. The juicer pipeline submits jobs to the cluster and then exits. It can therefore be run on the
  3 KB (369 words) - 16:29, 15 October 2023
• WGS Assembler
  ...ense. The pipeline revised for 454 data was named CABOG (Miller 2008). The pipeline revised for PacBio/Oxford was named 'PBcR' (Berlin 2015).
  3 KB (359 words) - 20:56, 12 August 2022
• PHYling
  Unified PHYling pipeline for phylogenomic data collection from annotated Stajich JE. 2017 PHYling: Phylogenomic pipeline from core markers on genomes to unassembled reads. https://github.com/staji
  3 KB (375 words) - 18:17, 3 June 2022
• Mikado
  [[Category:Pipeline]] Mikado is a lightweight Python3 pipeline to identify the most useful or
  4 KB (495 words) - 19:45, 18 August 2022
• Annocript
  Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes blast a ...cchia F, Basu S, Petrosino G, Salvemini M, Sanges R. Annocript: a flexible pipeline for the annotation of transcriptomes which can also identify putative long
  3 KB (387 words) - 21:18, 6 December 2019
• DAWGPAWS
  ...erformance computing environment providing a scalability that makes this a Pipeline to Annotate Whole-genome Sequences (PAWS). The flexibility of evidences tha ...cles/10.1186/1746-4811-5-8 JC Estill and JL Bennetzen. 2009. "The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes." Pl
  3 KB (381 words) - 21:20, 6 December 2019
• VirSieve
  [[Category:Pipeline]] Environmental Viral Detection pipeline. Contains VirSieveAlign, VirSieveGATK, VirSieveIVar, and VirSieveVEP applic
  5 KB (639 words) - 18:59, 14 December 2022
• Caper
  ...[https://github.com/ENCODE-DCC/hic-pipeline ENCODE Hi-C uniform processing pipeline]. Caper wraps Cromwell to run pipelines on multiple platforms like GCP (Goo
  3 KB (425 words) - 14:43, 11 October 2023
• UFCG
  UFCG (Universal Fungal Core Genes) is a pipeline that provides databases and methods for a genome-width taxonomic profiling ...& Steinegger, M. (2023) UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi. Nucleic Acids Research, 51(
  3 KB (431 words) - 17:41, 20 September 2023
• CellProfiler
  -p PIPELINE_FILENAME, --pipeline=PIPELINE_FILENAME Load this pipeline file on startup
  8 KB (910 words) - 21:29, 21 December 2022
• QTL-seq
  [[Category:Pipeline]] ...Booker, Hideki Innan, Ryohei Terauchi, Akira Abe (2020). High performance pipeline for MutMap and QTL-seq.[URL]
  3 KB (410 words) - 19:05, 31 January 2022
• Stacks
  Stacks is a software pipeline for building loci out of a set of short-read sequenced samples. Stacks was The command line pipeline is available via the "stacks" environment module.
  4 KB (658 words) - 21:20, 2 January 2023
• Fast-Plast
  Fast-Plast is a pipeline that leverages existing and novel programs to quickly assemble, orient, and ...sembly implemented in afin to close gaps of contigs with low coverage. The pipeline then identifies regions from the quadripartite structure of the chloroplast
  4 KB (487 words) - 21:20, 6 December 2019
• Mutmap
  Pipeline to identify causative mutations responsible for a phenotype.
  2 KB (236 words) - 16:06, 21 June 2023
• Orthologer
  OrthoDB standalone pipeline for delineation of orthologs
  2 KB (238 words) - 20:03, 31 May 2022
• EnTAP
  Description: Eukaryote Non-Model Transcriptome Annotation Pipeline
  2 KB (236 words) - 21:20, 6 December 2019
• BSseeker2
  A versatile aligning pipeline for bisulfite sequencing data.
  2 KB (238 words) - 14:40, 10 June 2022
• FRAMA
  Description: a transcriptome assembly and mRNA annotation pipeline
  2 KB (236 words) - 21:21, 6 December 2019
• Nullarbor
  Pipeline to generate complete public health microbiology reports from sequenced isol
  2 KB (241 words) - 19:38, 31 May 2022
• Scalpel
  Bioinformatics pipeline for discovery of genetic variants from NGS reads.
  2 KB (239 words) - 22:07, 21 August 2022
• LongRanger
  Phasing and SV Calling Pipeline
  2 KB (247 words) - 14:42, 10 June 2022
• SeCaPr
  A computational pipeline for processing Illumina sequence capture data
  2 KB (246 words) - 21:24, 6 December 2019
• AAFTF
  [[Category:Software]][[Category:Biology]][[Category:Pipeline]][[Category:Assembly]]
  2 KB (245 words) - 20:45, 11 August 2022
• FlowCraft
  FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦
  2 KB (246 words) - 14:18, 10 July 2020
• MAGeCKFlute
  MAGeCKFlute - Integrative analysis pipeline for pooled CRISPR functional genetic screens.
  2 KB (252 words) - 20:24, 15 August 2022
• Spacemake
  Spacemake: pipeline for processing and analysing sequencing based spatial-transcriptomics data
  2 KB (249 words) - 22:12, 22 September 2022
• MiRBShunter
  A pipeline to identify miRNA binding sites from Ago2-CLIP data by de novo motif findin
  2 KB (252 words) - 21:21, 6 December 2019
• CBGpipe
  This pipeline is designed to complete circular bacterial genomes using a sampling strateg
  2 KB (255 words) - 21:59, 26 August 2020
• Hyb
  Hyb is a bioinformatics pipeline for analysis of CLASH (crosslinking, ligation and sequencing of hybrids) da
  2 KB (247 words) - 15:07, 10 June 2022
• SqueezeMeta
  SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
  2 KB (255 words) - 15:47, 28 April 2022
• Rnaseqlib
  rnaseqlib is a simple, lightweight pipeline for RNA-Seq analysis.
  2 KB (247 words) - 15:15, 10 June 2022
• MAGeCK-VISPR
  MAGeCK-VISPR is a comprehensive quality control, analysis and visualization pipeline for CRISPR/Cas9 screens build on top of MAGeCK and VISPR.
  2 KB (251 words) - 20:21, 26 May 2022
• Hgtector
  HGTector is a computational pipeline for genome-wide detection of putative horizontal gene transfer (HGT) events
  2 KB (253 words) - 17:04, 10 October 2022
• MitoFinder
  Mitofinder is a pipeline to assemble mitochondrial genomes and extract mitochondrial genes from trim
  2 KB (255 words) - 21:23, 6 December 2019
• Quantas
  Quantas: A pipeline to analyze alternative splicing using RNA-Seq
  2 KB (247 words) - 20:29, 12 August 2022
• Varpipe-wgs
  This repository contains an analysis pipeline developed to characterize WGS output
  2 KB (261 words) - 16:22, 15 March 2023
• Mrtrix3tissue
  Improved bioinformatic pipeline to identify and quantify circRNA expression
  2 KB (255 words) - 16:51, 30 January 2023
• Toil
  Toil is a scalable, efficient, cross-platform pipeline management system, written entirely in Python, and designed around the prin
  2 KB (258 words) - 20:47, 12 August 2022
• Tapestri
  Pipeline developed by Mission Bio for the analysis of single-cell sequencing data in
  2 KB (258 words) - 19:07, 1 June 2022
• Merge peaks
  CWL-defined pipeline for using IDR to produce a set of peaks given two replicate eCLIP peaks
  2 KB (254 words) - 18:51, 15 August 2022
• BIRDS
  ...r efficient, versatile mapping of mouse brain）is an open source automation pipeline suitable for brain data from different microscopy platforms.
  2 KB (263 words) - 13:01, 15 August 2022
• FLEA
  |{{#vardefine:url|https://github.com/veg/flea-pipeline}} FLEA is a bioinformatics pipeline for analyzing longitudinal sequencing data from the Pacific Biosciences RS-
  2 KB (260 words) - 22:01, 27 August 2020
• Braker
  BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneM
  2 KB (261 words) - 22:28, 26 August 2020
• DeNoGAP
  Denovo Genome Analysis Pipeline for Prokaryotic Species
  2 KB (272 words) - 21:20, 6 December 2019
• Genmap
  Reginato M. 2022. A pipeline for assembling low-copy nuclear markers from plant genome skimming data for
  2 KB (256 words) - 21:20, 17 May 2023
• EPACTS
  ...and Parallelizable Association Container Toolbox) is a versatile software pipeline to perform various statistical tests for identifying genome-wide associatio
  2 KB (269 words) - 18:52, 12 August 2022
• TPP
  The Sashimi project develops the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics:
  2 KB (266 words) - 20:22, 24 August 2022
• NPhase
  [[Category:Pipeline]]
  2 KB (275 words) - 17:53, 15 August 2022
• Connectomemapper3
  Connectome Mapper 3 implements a full diffusion MRI processing pipeline that understands BIDS datasets, from raw Diffusion / T1 / T2 data to multi-
  2 KB (269 words) - 13:55, 15 August 2022
• TAPIS
  TAPIS (Transriptome Analysis Pipeline from Isoform Sequencing) is a program for correcting and aligning long read
  2 KB (273 words) - 16:14, 10 June 2022
• Ezaai
  ...link.springer.com/article/10.1007%2Fs12275-021-1154-0 Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity
  2 KB (282 words) - 15:13, 15 August 2022
• Shovill
  Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the pr
  2 KB (286 words) - 18:13, 23 August 2022
• Velocyto
  Velocyto includes a command line tool and an analysis pipeline
  2 KB (275 words) - 00:33, 25 May 2023
• Checkv
  CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identif
  2 KB (278 words) - 13:58, 18 October 2022
• GROCSVs
  ...Reconstruction of Complex Structural Variants, or GROC-SVs, is a software pipeline for identifying large-scale structural variants, performing sequence assemb
  2 KB (274 words) - 21:21, 6 December 2019
• Dragonflye
  Dragonflye is a pipeline that aims to make assembling Oxford Nanopore reads quick and easy. Still wo
  2 KB (283 words) - 20:18, 12 April 2022
• Blast2GO CLI
  ...igh-performance and automatic functional annotation tasks. This Annotation Pipeline allows your to integrate and automate your functional annotation task in a
  2 KB (282 words) - 20:19, 24 August 2022
• PhyloFlash
  phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition o
  2 KB (279 words) - 00:09, 29 October 2020
• Seekdeep
  The SeekDeep pipeline is intended for use on targeted amplicon sequencing data for haplotype freq
  2 KB (281 words) - 17:03, 24 July 2023
• FMRIPrep
  fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses
  2 KB (288 words) - 16:47, 17 October 2023
• Shortbred
  ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identify
  2 KB (287 words) - 16:12, 24 November 2020
• C-wap
  C-WAP is a bash-based bioinformatics pipeline for the analysis of either long-read (ONT or PacBio) or short-read (Illumin
  2 KB (281 words) - 13:16, 15 August 2022
• Fanc
  FAN-C provides a pipeline for analysing Hi-C data starting at mapped paired-end sequencing reads.
  2 KB (281 words) - 15:56, 22 March 2024
• CRISPResso2
  CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing exp
  2 KB (282 words) - 13:25, 11 October 2022
• Pggb
  This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation
  2 KB (287 words) - 19:56, 6 November 2020
• COLMAP
  ...a general-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline with a graphical and command-line interface. It offers a wide range of feat
  2 KB (290 words) - 16:53, 6 June 2022
• SibeliaZ
  construction pipeline. The blocks coordinates are output in GFF format and
  2 KB (284 words) - 20:40, 12 August 2022
• IRAP
  iRAP is a flexible RNA-seq analysis pipeline that allows the user to select and apply their preferred combination of exi
  2 KB (296 words) - 20:10, 24 August 2022
• Ciriquant
  CIRIquant is a comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data
  2 KB (275 words) - 15:00, 30 March 2022
• FastPlast
  Fast-Plast is a pipeline that leverages existing and novel programs to quickly assemble, orient, and
  2 KB (288 words) - 20:23, 23 May 2022
• Circompara2
  CirComPara2 is a computational pipeline to detect, quantify, and correlate expression of linear and circular RNAs f
  2 KB (283 words) - 21:36, 1 April 2022
• RiboTaper
  RiboTaper is a new analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet p
  3 KB (293 words) - 13:48, 20 May 2020
• Autometa
  An automated binning pipeline for single metagenomes, in particular host-associated and highly complex on
  3 KB (300 words) - 21:19, 6 December 2019
• Galaxyml
  Galaxy-ML is a web machine learning end-to-end pipeline building framework, with special support to biomedical data.
  2 KB (284 words) - 14:51, 27 January 2023
• SeqyClean
  ...genome assembly and mapping. We propose SeqyClean, a specialized cleaning pipeline that alleviates these issues.
  3 KB (312 words) - 22:41, 21 August 2022
• IAssembler
  ...sing Sanger and/or Roche-454 pyrosequencing technologies into contigs. The pipeline gives much higher accuracy in EST assembly than other existing assemblers b
  3 KB (301 words) - 18:39, 15 August 2022
• MetaLAFFA
  MetaLAFFA is a pipeline for annotating shotgun metagenomic data with abundances of functional ortho
  3 KB (305 words) - 13:52, 23 September 2021
• V-pipe
  ...onski K., Metzner K.J., and Beerenwinkel N. 2021. "V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput sequencing data.
  3 KB (296 words) - 17:20, 22 August 2022
• Bamtofastq
  ...l should contain the same set of sequences that were input to the original pipeline run, although the order will not be preserved. The FASTQs will be emitted i
  3 KB (318 words) - 13:56, 8 March 2021
• Popoolation
  PoPoolation is a pipeline for analysing pooled next generation sequencing data. Currently PoPoolation
  3 KB (321 words) - 21:23, 6 December 2019
• Tbprofiler
  The tbprofiler pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then
  3 KB (312 words) - 21:31, 10 February 2023
• SQANTI
  SQANTI is a pipeline for the in-depth characterization of isoforms obtained by full-length trans
  3 KB (321 words) - 21:24, 6 December 2019
• ProtHint
  ProtHint is a pipeline for predicting and scoring hints (in the form of
  3 KB (329 words) - 20:27, 12 August 2022
• Roary
  Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seema
  3 KB (308 words) - 17:13, 10 June 2022
• REPdenovo
  ...ies, and can generate much longer repeats than existing tools. The overall pipeline is shown in the mannual file. REPdenovo supports the following main functio
  3 KB (327 words) - 21:43, 21 August 2022
• LongStitch
  A genome assembly correction and scaffolding pipeline using long reads, consisting of up to three steps:
  3 KB (314 words) - 19:00, 10 October 2022
• ContaVect
  ...s from gene therapy vector production after NGS sequencing. This automated pipeline can however be used for wider purpose requiring to identify map NGS dataset
  3 KB (309 words) - 20:40, 10 June 2022
• PBJelly
  PBJelly is a highly automated pipeline that aligns long sequencing reads
  3 KB (309 words) - 17:07, 21 August 2022
• REAPR
  ...eference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an asse
  3 KB (320 words) - 21:35, 21 August 2022
• Ampligraph
  An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
  3 KB (315 words) - 14:44, 10 July 2023
• Necklace
  ...bly, in addition to using the reference annotation. Necklace is a software pipeline to run genome-guided and de novo assembly and combine the resulting transcr
  3 KB (312 words) - 21:22, 6 December 2019
• Pyrpipe
  ...pyrpipe_engine module to integrate any other third-party program in their pipeline.
  3 KB (311 words) - 15:22, 16 March 2020
• FEELnc
  This document is intended to give a technical description of the FEELnc pipeline in order to annotate long non-coding RNAs (lncRNAs) based on reconstructed
  3 KB (322 words) - 18:53, 10 July 2020
• Model Card Toolkit
  ...to a model's development and performance. Integrating the MCT into your ML pipeline enables the sharing model metadata and metrics with researchers, developers
  3 KB (333 words) - 15:31, 10 July 2023
• MarginPolish
  ...h serves as a standalone assembly polisher, it is also part of an assembly pipeline which includes an ultrafast nanopore assembler Shasta and a multi-task RNN
  3 KB (320 words) - 21:22, 6 December 2019
• FGMP
  FGMP (Fungal Genome Mapping Project) is a bioinformatic pipeline designed to provide in an unbiased manner an estimation of genome completen
  3 KB (326 words) - 21:20, 6 December 2019
• Methylpy
  Methylpy, a pyhton-based analysis pipeline for
  3 KB (309 words) - 21:21, 6 December 2019
• NpScarf
  ...draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing cluster as well as on a laptop computer for microbia
  3 KB (326 words) - 14:29, 4 September 2020
• CCMetagen
  CCMetagen is a pipeline to classify organisms in metagenomes or metatranscriptomes accurately.
  3 KB (327 words) - 22:45, 3 January 2022
• Crossmapper
  Crossmapper is an automated bioinformatics pipeline for asessing the rate of read crossmapping when two or more organisms are s
  3 KB (326 words) - 17:40, 31 January 2022
• Amphora2
  An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
  3 KB (333 words) - 17:35, 10 June 2022
• AMOS
  ...so that new contributions can be easily inserted into an existing assembly pipeline. This modular design will foster the development of new assembly algorithms
  3 KB (344 words) - 12:41, 12 August 2022
• Talon
  A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification. Dana Wyman, Gabriela Balder
  3 KB (321 words) - 15:13, 23 September 2022
• ElPrep
  ...of the number of processing steps that need to be applied in a particular pipeline, greatly improving runtime performance.
  3 KB (345 words) - 21:20, 6 December 2019
• Pdb2pqr
  *PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Dolinsky TJ
  3 KB (336 words) - 17:51, 15 August 2022
• AutoDock-GPU
  included a batched ligand pipeline developed by Aaron Scheinberg from
  3 KB (332 words) - 15:25, 12 August 2022
• Seqmule
  ...ent, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file. SeqMule al
  3 KB (342 words) - 19:06, 15 September 2022
• Finder
  finder is a gene annotator pipeline which automates the process of
  3 KB (345 words) - 16:42, 15 August 2022
• WU BLAST
  ...st error checking identifies problems sooner; flexible identifiers improve pipeline design and management
  3 KB (356 words) - 17:44, 22 August 2022
• Hapdup
  HapDup (haplotype duplicator) is a pipeline to convert a haploid long read assembly into a dual diploid assembly. The r
  3 KB (324 words) - 21:07, 7 April 2022
• Haplomerger2
  HM2 is an easy-to-use automated pipeline for improving geneome assembly in the post-assembly stage. It consists of a
  3 KB (339 words) - 19:05, 12 August 2022
• Hapsembler
  The Hapsembler pipeline is described in contain three main stages:
  3 KB (332 words) - 18:15, 15 August 2022
• Meraculous
  ...mble human-sized genomes on commodity clusters in under a day. The process pipeline implements a highly transparent and portable model of job control and monit
  3 KB (354 words) - 18:36, 10 June 2022
• Rapidsai
  ...at integrates with a variety of machine learning algorithms for end-to-end pipeline accelerations without paying typical serialization costs. RAPIDS also inclu
  3 KB (348 words) - 21:29, 21 August 2022
• READemption
  READemption is a pipeline for the computational evaluation of RNA-Seq data. It was originally develop
  3 KB (352 words) - 17:58, 1 June 2022
• Nipype
  existing pipeline systems.
  3 KB (348 words) - 20:07, 12 August 2022
• Humann2
  HUMAnN 2.0 is a pipeline for efficiently and accurately profiling the presence/absence and abundance
  3 KB (348 words) - 22:26, 27 August 2020
• Aquamis
  AQUAMIS is a pipeline for routine assembly and quality assessment of microbial isolate sequencing
  3 KB (348 words) - 22:07, 20 October 2023
• PanX
  ...n-genome analysis, interactive visualization and exploration. The analysis pipeline is based on DIAMOND (Buchfink et al. 2015 Nature Methods), MCL and phylogen
  3 KB (346 words) - 21:22, 6 December 2019
• Biolite
  * A modular 'pipeline' framework with Python wrappers and workflows for commonly used NGS tools,
  3 KB (362 words) - 12:54, 15 August 2022
• RDnaTools
  ...ily the Mothur suite of utilities. Currently rDnaTools implements a single pipeline for the export, filtering, and cluster of 16S sequences.
  3 KB (361 words) - 21:24, 6 December 2019
• Mantis
  ...m needs a tumor BAM and a matched normal BAM file (produced using the same pipeline) to determine the instability score between the two samples within the pair
  3 KB (368 words) - 17:20, 27 May 2022
• Chewbbaca
  chewBBACA “BSR-Based Allele Calling Algorithm” is a comprehensive pipeline including a set of functions for the creation and validation of whole genom
  3 KB (346 words) - 15:58, 20 October 2023
• VirusDetect
  ...z D, Fuentes S, Ling K-S, Kreuze J, Fei Z (2017) VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs.]
  3 KB (377 words) - 23:22, 30 July 2020
• BiG-SCAPE
  ...ategory:Phylogenetics]][[Category:Biology]][[Category:Genomics]][[Category:Pipeline]]
  3 KB (377 words) - 12:53, 15 August 2022
• Blast2GO
  The Blast2GO Pipeline Version (B2G4Pipe) runs Blast2GO without graphical interface. The pipeline accepts BLAST and InterProScan results and parses
  6 KB (920 words) - 14:08, 16 March 2023
• Haphpipe
  HAplotype and PHylodynamics pipeline for viral assembly, population genetics, and phylodynamics.
  3 KB (405 words) - 16:40, 14 March 2023
• SNAP
  SNAP is a program that is part of a gene sequencing pipeline. It takes data from gene sequencing hardware that consists of short chunks
  3 KB (372 words) - 20:42, 12 August 2022
• SRAssembler
  SRAssembler (Selective Recursive local Assembler) is a modular pipeline program that can assemble genomic DNA reads into contigs that are homologou
  3 KB (381 words) - 15:33, 27 May 2022
• Deepvariant
  DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generati
  3 KB (356 words) - 18:49, 12 August 2022
• Wgs
  ...rge in 2004 as the wgs-assembler under the GNU General Public License. The pipeline revised for 454 data was named CABOG (Miller 2008).
  3 KB (375 words) - 20:55, 12 August 2022
• PerM
  ...ormat and that output can be further processed by ComB, SAMtools, RseqFlow pipeline and the [[Galaxy]]. Check the [http://code.google.com/p/perm/wiki/Manual ma
  3 KB (396 words) - 17:40, 21 August 2022
• Themisto
  ...Epidemiology with Mixed Samples. Supplement: Pseudoalignment in the mGEMS pipeline.
  3 KB (401 words) - 20:57, 3 June 2022
• MetaWRAP
  ...efull in your research, please cite the publication: MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis. If certain software wrapped
  3 KB (412 words) - 22:31, 8 September 2020
• Circos
  ...corporated into data acquisition, analysis and reporting pipelines (a data pipeline is a multi-step process in which data is analyzed by multiple and typically
  3 KB (409 words) - 13:35, 15 August 2022
• Maker
  MAKER is a portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic and prokaryotic genome project
  3 KB (387 words) - 18:20, 18 August 2022
• GRIDSS
  ...t is hoped that GRIDSS can serve as an exemplar modular structural variant pipeline designed for interoperability with other tools.
  3 KB (388 words) - 21:20, 6 December 2019
• ARC
  ARC is a pipeline which facilitates iterative, reference guided ''de novo'' assemblies with t
  3 KB (430 words) - 14:32, 12 August 2022
• YAGO
  This is the pipeline to run YAGO 4. It allows to build YAGO 4 from a Wikidata dump.
  4 KB (480 words) - 17:13, 15 December 2022
• Amrfinderplus
  ...mbled nucleotide sequence. AMRFinderPlus is used in the Pathogen Detection pipeline, and these data are displayed in NCBI’s Isolate Browser. AMRFinderPlus re
  4 KB (447 words) - 15:59, 27 May 2022
• EDTA
  ...le Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline. Genome Biol. 20(1): 275.]
  4 KB (474 words) - 21:27, 14 September 2023
• Sickle
  ...ion is close. Illumina quality refers to qualities encoded with the CASAVA pipeline between versions 1.3 and 1.7. Illumina quality using CASAVA >= 1.8 is Sange
  4 KB (551 words) - 22:56, 21 August 2022
• Trimmomatic
  ...(using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used), either uncompressed or gzipp'ed FASTQ. Use of gzip format is determi
  4 KB (522 words) - 20:52, 12 August 2022
• Galaxy
  ...ed collaborative environment, Galaxy's work history sharing and analytical pipeline building, as well as publishing and sharing the results in a convenient and
  4 KB (562 words) - 18:05, 9 November 2022
• Appreci8
  Appreci8 is a variant calling pipeline for detecting single nucleotide variants (SNVs) and short indels (up to 30
  4 KB (561 words) - 14:25, 12 August 2022
• GATK
  ...plementary tools to those available in those two packages. Our SNP calling pipeline (Q score recalibration -> multiple sequence realignment -> snp/index callin
  4 KB (540 words) - 16:53, 15 August 2022
• Biology
  ...turn, will provide the hardware and software support for the data analysis pipeline they create for you.
  4 KB (665 words) - 21:23, 14 December 2022
• Parabricks
  ...line and somatic analysis. The core of the Parabricks software is its data pipeline which takes raw data and transforms it according to the user's requirements
  4 KB (574 words) - 21:25, 14 December 2022
• Rnalysis
  If you use the Limma-Voom differential expression pipeline in your research, please cite:
  5 KB (648 words) - 16:12, 25 April 2023
• AlphaFold
  This package provides an implementation of the inference pipeline of AlphaFold v2.3. This is a completely new model that was entered in CASP1
  6 KB (832 words) - 15:38, 2 February 2024
• OrthoMCL
  ...-- that creates a suitable orthomcl.config file and automates much of the pipeline is provided:
  5 KB (748 words) - 22:40, 28 January 2024

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