3.0.0

Rasusa container

Main tool : Rasusa

Additional tools:

• none

Full documentation: https://github.com/mbhall88/rasusa

Randomly subsample sequencing reads to a specified coverage.

Note that rasusa requires certain parameters:

• -c, --coverage, which can be supplemented by (-b, --bases), (-n, --num), and (-f, --frac) in reads, but is required for aln
• -g, --genome-size, which can be supplemented by (-b, --bases), (-n, --num), and (-f, --frac) in reads, and is not an argument for aln.
• input
  • Valid FASTA or FASTQ format for the reads command
  • Valid coordinate-sorted SAM/BAM/CRAM for the aln command
  • Can be compressed via gzip
  • If 2 inputs are passed to reads, it is assumed they are paired-end reads.

Note: Version 3.0.0 introduces a major change from versions < 3.0.0.

• deps: Subsampling results for a fixed seed will differ from versions < 3.0.0. This is caused by internal algorithmic changes in the rand crate (0.8.5 -> 0.10.0) and requires a major version bump.

Example Usage

# sars-cov-2 example, paired-end illumina
rasusa reads \
       -n 40434 \          # downsample to specific number of reads per FASTQ file
       -s 1 \              # set seed 
       -O g \              # set output file compression format as gzip
       -o SRR13957123_downsampled_1.fastq.gz -o SRR13957123_downsampled_2.fastq.gz \
       SRR13957123_1.fastq.gz SRR13957123_2.fastq.gz

# Salmonella enterica example, paired-end illumina
rasusa reads \
       --coverage 100 \    # use 100X coverage for downsampling
       --genome-size 5M \  # downsample to specific coverage based on genome size (5 million bases)
       -s 1 \              # set seed 
       -O g \              # set output file compression format as gzip
       -o SRR10992628_downsampled_1.fastq.gz -o SRR10992628_downsampled_2.fastq.gz \
       SRR10992628_1.fastq.gz SRR10992628_2.fastq.gz