Search results

• 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

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