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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

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