Metagenomic workflow with Snakemake

In the provided directory, you will find paired Illumina reads for two different samples: PWG269 & ZQV658 - *_1.fastq.gz denote the forward reads and *_2.fastq.gz denote the reverse reads.

The task:

• Map the sample reads onto the three genomes provided in the subdirectory genomes/

• Provide an estimated relative abundance of the genomes in the two samples

• Relative abundance = no. of reads mapping to a genome / total reads in metagenome

• Provide a output TSV file called consolidated_data.tsv that combines the results for both samples with the following header format:

  Genome  Relative Abundance      sample_id       species_name
  

  • where 'Genome' matches the values in the list genomes or the keys of the dictionary names as decribed in mapping-workflow.smk
  • 'sample_id' consists of either PWG269 & ZQV658
  • 'species_name' consists of the values in the dictionary names as decribed in mapping-workflow.smk

Results

To run the script:

snakemake --snakefile mapping-workflow.smk

This is the workflow created with Snakemake:

Mapping results:

Genome	Relative Abundance	sample_id	species_name
AEKH01.1_genomic	0.001661396554378590	PWG269	Lactobacillus iners
CAAKNZ01.1_genomic	0.6488379529293530	PWG269	Bifidobacterium breve
GCF_902381625.1_genomic	0.349500650516268	PWG269	Bifidobacterium longum
AEKH01.1_genomic	0.00240733861268147	ZQV658	Lactobacillus iners
CAAKNZ01.1_genomic	0.24584830640326300	ZQV658	Bifidobacterium breve
GCF_902381625.1_genomic	0.7517443549840550	ZQV658	Bifidobacterium longum