Downsample data by barcode

While downsampling (subsampling) FASTQ and BAM files is relatively simple with tools such as awk, samtools, seqtk, seqkit, etc., downsample allows you to downsample a BAM file (or FASTQ(s)) by barcodes. That means you can keep all the reads associated with -d number of barcodes or fraction of barcodes (e.g. -d 0.5 will downsample to 50% of all barcodes).

FASTQ

usage
djinn fastq sample -d <value> [-i] PREFIX INPUT

example | downsample fastq pair, including invalid barcodes
djinn fastq sample -d 1000 -i sample1.sub1000 sample1.F.fq.gz sample1.R.fq.gz

Running Options

argument	description
`INPUT`	required A FASTQ file or file pair
`-c` `--cache-size`	hidden number of reads to store before writing (bigger is faster, default: `10000`)
`-d` `--downsample`	required Number/fraction of barcodes to downsample to
`-i` `--invalid`	Include this proportion of invalid barcodes in downsampling
`-r` `--random-seed`	Random seed for sampling optional
`-t` `--threads`	Number of threads to use for writing compressed output fastq files (default: 2)

SAM

usage
djinn sam sample -d <value> [-i] INPUT > output.bam

example | downsample bam file by 50% of the barcodes, ignoring invalid barcodes
djinn sam sample -t 8 -d 0.5 -b BC sample1.bam > sample1.half.bam

Running Options

argument	description
`INPUT`	required SAM/BAM file
`-d` `--downsample`	required Number/fraction of barcodes to downsample to
`-i` `--invalid`	Include invalid barcodes in downsampling
`-r` `--random-seed`	Random seed for sampling optional
`-t` `--threads`	Number of threads to use (default: 4)