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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

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