Remove singletons or invalid barcodes

You may be interested in retaining only "useful" linked reads, that is, reads with a valid barcode or reads that are not singletons (i.e. there are more than 2 reads with the same barcode). Like their names suggests, filter-invalid will remove invalid barcodes and filter-singletons will remove singletons. Each of these commands can optionally retain the removed reads in separate files.

FASTQ

filter-invalid

usage
djinn fastq filter-invalid [--invalid] PREFIX INPUTS...

example | remove invalid barcodes and retain them in separate files
djinn fastq filter-invalid --invalid echidna_valid echidna.R1.fq.gz echidna.R2.fq.gz

Running Options

argument	description
`PREFIX`	required output filename prefix
`INPUTS`	required FASTQ or file pair
`-c` `--cache-size` hidden number of reads to store before writing (bigger is faster, default: `10000`)
`-i` `--invalid`	write reads with invalid barcodes to `prefix.invalid.bam` or `prefix.invalid.R[12].fq.gz`

filter-singletons

usage
djinn fastq filter-singletons [--singletons] PREFIX INPUT...

example | remove singleton barcodes and retain them in separate files
djinn fastq filter-singletons --singletons hyena_filt hyena.R1.fq.gz hyena.R2.fq.gz

Running Options

argument	description
`PREFIX`	required output filename prefix
`INPUT`	required FASTQ file or file pair
`-c` `--cache-size`	hidden number of reads to store before writing (bigger is faster, default: `10000`)
`-s` `--singletons`	write reads with singleton barcodes to `prefix.singletons.R[12].fq.gz`

SAM

filter-invalid

usage
djinn sam filter-invalid [--invalid] INPUT > output.bam

example | remove invalid barcodes and retain them in a separate file
djinn sam filter-invalid --invalid echidnda.invalid.bam echidna.bam > echidna.filtered.bam

Running Options

argument	description
`INPUT`	required SAM/BAM file
`-i` `--invalid`	output records with invalid barcodes to this file

filter-singletons

usage
djinn sam filter-singletons [--singletons] PREFIX INPUT > output.bam

example | remove singleton barcodes and retain them in a separate file
djinn sam filter-singletons --singletons hyena.singles.bam hyena.bam > hyena.filter.bam

Running Options

argument	description
`INPUTS`	required SAM/BAM file
`-s` `--singletons`	write valid singleton records to this file