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

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