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  • |{{#vardefine:app|snp-pipeline}} |{{#vardefine:url|https://github.com/CFSAN-Biostatistics/snp-pipeline}}
    3 KB (304 words) - 21:24, 6 December 2019
  • 3 KB (312 words) - 21:24, 6 December 2019
  • 4 KB (502 words) - 21:24, 6 December 2019

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  • ...line also supports detailed error reporting and easy resuming of runs. The pipeline has been tested on human, mouse and yeast ATAC-seq data and human and mouse ...ATAC-seq pipeline protocol definition is here. Some parts of the ATAC-seq pipeline were developed in collaboration with Jason Buenrostro, Alicia Schep and Wil
    3 KB (440 words) - 21:13, 6 December 2019
  • |{{#vardefine:app|snp-pipeline}} |{{#vardefine:url|https://github.com/CFSAN-Biostatistics/snp-pipeline}}
    3 KB (304 words) - 21:24, 6 December 2019
  • ...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
  • [[Category:Pipeline]] Lazypipe is a stand-alone pipeline for identifying viruses in host-associated or environmental samples. The ma
    4 KB (486 words) - 12:59, 1 June 2021
  • ...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 (338 words) - 21:24, 6 December 2019
  • 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) - 22:13, 27 August 2020
  • 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
  • PhyloPhlAn is a computational pipeline for reconstructing highly accurate and resolved phylogenetic trees based on The pipeline is scalable to thousands of genomes and uses the most conserved 400 protein
    3 KB (293 words) - 21:23, 6 December 2019
  • ...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
  • ...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 (291 words) - 21:20, 6 December 2019
  • RepeatExplorer is a computational pipeline for discovery and characterization of repetitive sequences in eukaryotic genomes. The pipeline
    2 KB (278 words) - 21:24, 6 December 2019
  • 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 (298 words) - 21:22, 6 December 2019
  • 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
  •   HomBlocks is a new and highly efficient pipeline that used homologous blocks searching method to construct multi-gene alignm   In this pipeline, the core conserved fragment (conserved coding genes, functional non-coding
    4 KB (478 words) - 21:21, 6 December 2019
  • ...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 (361 words) - 21:29, 6 December 2019
  • 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 (377 words) - 12:01, 1 July 2021

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