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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

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