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marsq's Introduction

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marsQ

Metagenomes against Reference Sequences Quantification

nf-core/marsq nf-core/marsq

Introduction

In development

nf-core/marsq is a bioinformatics pipeline that ...

  1. Read QC (FastQC)
  2. Present QC for raw reads (MultiQC)
  3. Maps reads agains reference genomes
  4. Quantifies

Usage

Reccomended running in the marsQ_slurm.sh

nextflow run main.nf \
        -w "${workdir}/work" \
        -profile singularity_slurm \
        -with-trace "logs/${SLURM_JOB_ID}.trace.txt" \
        --pipeline map_only \
        --reads "${workdir}/fastq/*{R1,R2}.fastq.gz" \
        --outdir "${workdir}/results" \
        --ref_genomes_folder "${workdir}/refs" \
        -resume

refs is a folder containing genomes to map against. One file per genome. A useful tool to download a range of sequences is genome_updater

marsq's People

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