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  • 8 members (0 subcategories, 0 files) - 19:41, 27 May 2022
  • |{{#vardefine:app|snp-pipeline}} |{{#vardefine:url|https://github.com/CFSAN-Biostatistics/snp-pipeline}}
    3 KB (306 words) - 17:00, 10 June 2022
  • 4 KB (501 words) - 18:55, 6 June 2022

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  • |{{#vardefine:app|snp-pipeline}} |{{#vardefine:url|https://github.com/CFSAN-Biostatistics/snp-pipeline}}
    3 KB (306 words) - 17:00, 10 June 2022
  • |{{#vardefine:url|https://github.com/GATB/gatb-minia-pipeline}} GATB-Minia-Pipeline is a de novo assembly pipeline for Illumina data. It can assemble genomes and metagenomes.
    2 KB (285 words) - 13:31, 15 August 2022
  • ...GERT utilizes several established bioinformatic tools combined into single pipeline which hides different technical quirks from an inexperienced user. ....com/articles/10.1186/s13100-019-0163-6 Guliaev AS, Semyenova SK. MGERT: a pipeline to retrieve coding sequences of mobile genetic elements from genome assembl
    3 KB (305 words) - 14:20, 15 September 2020
  • ...line, SNPhylo, to construct phylogenetic tree based on SNP data. With this pipeline, user can construct a phylogenetic tree from a file containing huge SNP dat Lee, T. H., Guo, H., Wang, X., Kim, C., & Paterson, A. H. (2014). SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics, 15(1).
    3 KB (340 words) - 17:48, 10 June 2022
  • [[Category:Pipeline]] The NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate
    3 KB (393 words) - 14:29, 6 July 2022
  • ...er determine the proper assignment of any remaining ambiguous contigs. The pipeline will run on either a haploid assembly (i.e. Canu, FALCON or FALCON-Unzip pr The pipeline is published at BMC Bioinformatics:
    3 KB (356 words) - 20:27, 12 August 2022
  • This package contains the pipeline for conducting a CUT&RUN analysis. The pipeline comprises of read trimming, alignment steps, motif finding steps, and final
    2 KB (266 words) - 22:20, 26 August 2020
  • ...ogy Meta Annotator for Plants (GOMAP) pipeline. GOMAP is a high-throughput pipeline to annotate GO terms to plant protein sequences.
    2 KB (263 words) - 17:17, 15 August 2022
  • Easy-to-use pipeline for the comprehensive metabolic annotation of microbial genomes. ...0-5 MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes]
    2 KB (270 words) - 17:52, 15 August 2022
  • Lazypipe is a stand-alone pipeline for identifying viruses in host-associated or environmental samples. The ma ...ifying viruses in host-associated or environmental samples. The Unix based pipeline for automated assembling and taxonomic profiling of NGS libraries has been
    4 KB (482 words) - 19:46, 15 August 2022
  • RepeatExplorer is a computational pipeline for discovery and characterization of repetitive sequences in eukaryotic genomes. The pipeline
    2 KB (278 words) - 20:31, 12 August 2022
  • The pipeline was originally developed for Illumina data, but thanks to the versatility o [https://academic.oup.com/nar/article/41/13/e129/1129833 MITObim pipeline described in Hahn et al. 2013]
    3 KB (301 words) - 15:20, 22 April 2020
  • zUMIs is a fast and flexible pipeline to process RNA-seq data with (or without) UMIs. The input to this pipeline is simply fastq files. In the most common cases, you will have a read conta
    2 KB (298 words) - 22:24, 26 August 2020
  • [[Category:Pipeline]] Environmental Viral Detection pipeline. Contains VirSieveAlign, VirSieveGATK, VirSieveIVar, and VirSieveVEP applic
    4 KB (451 words) - 19:58, 27 May 2022
  • ...bly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long rea
    2 KB (292 words) - 21:29, 6 December 2019
  • ...nd preparation. This is both a GUI and command line tool. The configurable pipeline includes image/diffusion information check, padding/Cropping of data, slice
    2 KB (290 words) - 21:50, 27 August 2020
  • The RADOrgMiner pipeline is designed to genotype sequence tags found in reduced genomic complexity l ...to draw a bright needle out from the haystack -- RADOrgMiner, an automated pipeline to genotype organellar reads from RADseq data. Authorea preprint. September
    3 KB (297 words) - 21:55, 6 July 2022
  • 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 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 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 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
  • [[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
  • 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 (339 words) - 16:41, 24 February 2022
  • ...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
  • ...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
  • 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
  • [[Category:Pipeline]] Mikado is a lightweight Python3 pipeline to identify the most useful or
    4 KB (493 words) - 19:39, 3 June 2022
  • 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
  • ...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
  • -p PIPELINE_FILENAME, --pipeline=PIPELINE_FILENAME Load this pipeline file on startup
    8 KB (889 words) - 13:24, 15 August 2022
  • [[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 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 (648 words) - 20:44, 12 August 2022
  • 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
  • OrthoDB standalone pipeline for delineation of orthologs
    2 KB (238 words) - 20:03, 31 May 2022
  • Bioinformatics pipeline for discovery of genetic variants from NGS reads.
    2 KB (237 words) - 19:49, 10 June 2022
  • Description: Eukaryote Non-Model Transcriptome Annotation Pipeline
    2 KB (236 words) - 21:20, 6 December 2019
  • A versatile aligning pipeline for bisulfite sequencing data.
    2 KB (238 words) - 14:40, 10 June 2022
  • Description: a transcriptome assembly and mRNA annotation pipeline
    2 KB (236 words) - 21:21, 6 December 2019
  • Pipeline to generate complete public health microbiology reports from sequenced isol
    2 KB (241 words) - 19:38, 31 May 2022
  • Phasing and SV Calling Pipeline
    2 KB (247 words) - 14:42, 10 June 2022
  • A computational pipeline for processing Illumina sequence capture data
    2 KB (246 words) - 21:24, 6 December 2019
  • [[Category:Software]][[Category:Biology]][[Category:Pipeline]][[Category:Assembly]]
    2 KB (245 words) - 20:45, 11 August 2022
  • FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦
    2 KB (246 words) - 14:18, 10 July 2020
  • MAGeCKFlute - Integrative analysis pipeline for pooled CRISPR functional genetic screens.
    2 KB (252 words) - 20:24, 15 August 2022
  • 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
  • This pipeline is designed to complete circular bacterial genomes using a sampling strateg
    2 KB (255 words) - 21:59, 26 August 2020
  • 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: a fully automated metagenomics pipeline, from reads to bins
    2 KB (255 words) - 15:47, 28 April 2022
  • rnaseqlib is a simple, lightweight pipeline for RNA-Seq analysis.
    2 KB (247 words) - 15:15, 10 June 2022
  • 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
  • Mitofinder is a pipeline to assemble mitochondrial genomes and extract mitochondrial genes from trim
    2 KB (255 words) - 21:23, 6 December 2019
  • Quantas: A pipeline to analyze alternative splicing using RNA-Seq
    2 KB (247 words) - 20:29, 12 August 2022
  • 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
  • Pipeline developed by Mission Bio for the analysis of single-cell sequencing data in
    2 KB (258 words) - 19:07, 1 June 2022
  • 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
  • ...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
  • |{{#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 is a pipeline for fully automated prediction of protein coding gene structures with GeneM
    2 KB (261 words) - 22:28, 26 August 2020
  • Denovo Genome Analysis Pipeline for Prokaryotic Species
    2 KB (272 words) - 21:20, 6 December 2019
  • ...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
  • 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) - 20:01, 10 June 2022
  • [[Category:Pipeline]]
    2 KB (275 words) - 17:53, 15 August 2022
  • 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 (Transriptome Analysis Pipeline from Isoform Sequencing) is a program for correcting and aligning long read
    2 KB (273 words) - 16:14, 10 June 2022
  • ...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
  • ...lyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools f
    2 KB (273 words) - 19:12, 15 August 2022
  • ...igh-performance and automatic functional annotation tasks. This Annotation Pipeline allows your to integrate and automate your functional annotation task in a
    2 KB (280 words) - 18:17, 12 August 2022
  • ...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
  • fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses
    2 KB (281 words) - 14:16, 6 June 2022
  • 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
  • phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition o
    2 KB (279 words) - 00:09, 29 October 2020
  • 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 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
  • 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
  • ...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
  • construction pipeline. The blocks coordinates are output in GFF format and
    2 KB (284 words) - 20:40, 12 August 2022
  • CIRIquant is a comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data
    2 KB (275 words) - 15:00, 30 March 2022
  • 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
  • iRAP is a flexible RNA-seq analysis pipeline that allows the user to select and apply their preferred combination of exi
    2 KB (298 words) - 19:02, 15 August 2022
  • 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 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
  • An automated binning pipeline for single metagenomes, in particular host-associated and highly complex on
    3 KB (300 words) - 21:19, 6 December 2019
  • ...genome assembly and mapping. We propose SeqyClean, a specialized cleaning pipeline that alleviates these issues.
    3 KB (306 words) - 16:52, 10 June 2022
  • ...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 is a pipeline for annotating shotgun metagenomic data with abundances of functional ortho
    3 KB (305 words) - 13:52, 23 September 2021
  • ...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 is a pipeline for analysing pooled next generation sequencing data. Currently PoPoolation
    3 KB (321 words) - 21:23, 6 December 2019
  • ...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 (297 words) - 18:51, 15 August 2022
  • 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 is a pipeline for predicting and scoring hints (in the form of
    3 KB (329 words) - 20:27, 12 August 2022
  • 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
  • ...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) - 17:18, 10 June 2022
  • A genome assembly correction and scaffolding pipeline using long reads, consisting of up to three steps:
    3 KB (314 words) - 21:33, 8 August 2022
  • PBJelly is a highly automated pipeline that aligns long sequencing reads
    3 KB (307 words) - 20:18, 12 August 2022
  • ...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
  • ...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
  • ...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) - 17:24, 10 June 2022
  • ...pyrpipe_engine module to integrate any other third-party program in their pipeline.
    3 KB (311 words) - 15:22, 16 March 2020
  • 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
  • ...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

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