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» nextflow run nf-core/kmermaid -profile test
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Introduction

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Documentation

The nf-core/kmermaid pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting

Usage

With a samples.csv file:

nextflow run nf-core/kmermaid --outdir s3://olgabot-maca/nf-kmer-similarity/ --samples samples.csv

With R1, R2 read pairs:

nextflow run nf-core/kmermaid --outdir s3://olgabot-maca/nf-kmer-similarity/ \
  --read_pairs 's3://olgabot-maca/sra/homo_sapiens/smartseq2_quartzseq/*{R1,R2}*.fastq.gz,s3://olgabot-maca/sra/danio_rerio/smart-seq/whole_kidney_marrow_prjna393431/*{1,2}.fastq.gz'

With SRA ids:

nextflow run nf-core/kmermaid --outdir s3://olgabot-maca/nf-kmer-similarity/ --sra SRP016501

With fasta files:

nextflow run nf-core/kmermaid --outdir s3://olgabot-maca/nf-kmer-similarity/ \
  --fastas '*.fasta'

With bam file

nextflow run czbiohub/nf-kmer-similarity --outdir s3://olgabot-maca/nf-kmer-similarity/ \
  --bam 'possorted_genome_bam.bam'

With split kmer

nextflow run czbiohub/nf-kmer-similarity --outdir s3://olgabot-maca/nf-kmer-similarity/ --samples samples.csv --splitKmer --subsample 1000

Credits

nf-core/kmermaid was originally written by Olga Botvinnik.