ammaraziz / sipe

Snakemake Illumina Pipeline for Entero - sipe

Overview

1. fastp - trim and qc
2. blast - blast reads against vp1 reference
3. Bowtie2 - Align to full genome nr entero reference set
4. ivar - create consensus

Inputs

• config.yaml

  • out_dir: path to output directory
  • reference_wgf: path to reference for alignment
  • reference_blast: path to blast database
  • bed_file: path to primer bed files - not used

• samples.tsv

  • columns: forward reverse sample sample_library

Outputs

1. See analysis/ folder
   • qc/{sample}.{pair}.fastq.gz - qc'ed fastq
   • qc/{sample}.html
   • blast/{sample}.xml - blast results
   • align/{sample}/{sample}.bam
   • consensus/{sample}/{sample}.consensus.fasta
   • depth/{sample}.depth.txt
   • depth/{sample}.pdf

Install

Install conda/mamba and snakeamke

mamba create -c bioconda -c conda-forge snakemake

Run:

Navigate to sipe/ then run:

snakemake -j {cpu} --use-conda

Snakemake will handle the dependency installation.

Depends

Install in order:

1. conda/mamba
2. ivar
3. bowtie2
4. samtools
5. bamtools
6. fastp