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https://github.com/acvill/phagepipeline

Turner Lab phage assembly and annotation pipeline

https://github.com/acvill/phagepipeline

Science Score: 13.0%

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    Low similarity (6.3%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Turner Lab phage assembly and annotation pipeline

Basic Info
  • Host: GitHub
  • Owner: acvill
  • Language: Shell
  • Default Branch: master
  • Size: 20.5 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Created about 2 years ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

A pipeline for assembling and annotating phage genomes. This pipeline is hard-coded to make use of the YCRC's software modules and dSQ job submission system.

```{bash}

create an alias

echo "alias PhagePipeline='sh ~/project/sharedscripts/PhagePipeline/runPhagePipeline.sh'" >> ~/.bashrc

test the pipeline

PhagePipeline {bash} Usage: sh runPhagePipeline.sh -f

-s [-o,-d,-g,-m,-q,-k] -h print this usage statement and exit -f REQUIRED - path containing paired-end sequencing files Assumes filenames are structured as R1.fastq[.gz] and _R2.fastq[.gz] -s REQUIRED - bowtie2 index for host read removal (either 'PAO1', 'PA14', or path to custom index) -o output path (default: pwd) -d read subsampling depth for shovill assembly (default: 150) -g estimated genome size for shovill assembly (as , default: 100K) -m minimum contig length to keep (default: 1000) -q quoted parameter string for dSQ job array Must use long option names (default: '--partition scavenge --requeue --mem 20g --cpus-per-task 8 --time 6:00:00') -k keep all temporary / intermediate files (exclude to delete tmp folder) ```

Owner

  • Name: Albert Vill
  • Login: acvill
  • Kind: user
  • Location: Connecticut, USA

PhD in metagenomics. Currently in the Turner Lab at Yale

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