umitools

Tools to handle reads sequenced with unique molecular identifiers (UMIs).

Trim the UMI

Incorporate the UMI into the read name in order to later identify while processing mapped reads.

umitools trim --end 5 unprocessed_fastq NNNNNV > out.fq

Remove Duplicates

For any given start site, save only one read per UMI. Writes bed3+ to stdout with before and after counts per start.

umitools rmdup unprocessed.bam out.bam > before_after.bed

Specifying --mismatches will, for a given start site, merge all UMIs within that edit distance into a single unique hit. For example, if a new UMI is within a single mismatch of any existing observed UMIs for a start position, it will be merged and considered a duplicate. The mismatch can occur at any position, regardless of the IUPAC sequence you're using.

Requires

pip install pysam editdist