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Category:Pipeline

8 members (0 subcategories, 0 files) - 15:27, 23 August 2022
SNP-Pipeline
|{{#vardefine:app|snp-pipeline}} |{{#vardefine:url|https://github.com/CFSAN-Biostatistics/snp-pipeline}}

3 KB (306 words) - 17:00, 10 June 2022
Ssr pipeline

4 KB (501 words) - 18:55, 6 June 2022

Page text matches

Geomxngspipeline
...in the Configuration File (which is generated from the GeoMx DSP run). The Pipeline processes information from these files and outputs .dcc files, which can th * The pipeline must be run in an interactive session because of an interactive prompt for

3 KB (332 words) - 17:51, 29 January 2024
SNP-Pipeline
|{{#vardefine:app|snp-pipeline}} |{{#vardefine:url|https://github.com/CFSAN-Biostatistics/snp-pipeline}}

3 KB (306 words) - 17:00, 10 June 2022
Minia
|{{#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
MGERT
...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
SNPhylo
...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
PGAP
[[Category:Pipeline]] The NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate

3 KB (393 words) - 14:29, 6 July 2022
Purge haplotigs
...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
CutRunTools
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
GOMAP
...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
MicrobeAnnotator
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) - 19:02, 10 October 2022
Lazypipe
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 (507 words) - 16:54, 14 December 2022
RepeatExplorer
RepeatExplorer is a computational pipeline for discovery and characterization of repetitive sequences in eukaryotic genomes. The pipeline

2 KB (278 words) - 21:44, 21 August 2022
Circexplorer3
A computational pipeline for Circular and Linear RNA Expression Analysis from Ribosomal-RNA depleted Ma XK*, Wang MR, Liu CX, Dong R, Carmichael GG, Chen LL and Yang L#. A CLEAR pipeline for direct comparison of circular and linear RNA expression. 2019, bioRxiv

2 KB (271 words) - 15:06, 18 January 2023
MITObim
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
Unicycler
...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
Panaroo
panaroo is a pipeline for pangenome investigation. ...rkhill J. 2020. Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biol 21:180.]

2 KB (289 words) - 19:33, 13 June 2023
ZUMIS
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 (302 words) - 17:55, 22 August 2022
Bactopia
Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to proc Petit III RA, Read TD, Bactopia: a flexible pipeline for complete analysis of bacterial genomes. mSystems. 5 (2020), https://doi

2 KB (292 words) - 21:38, 10 January 2023
Dtiprep
...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
Radorgminer
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
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

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