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

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

If you want to save reads with invalid UMI sequences, you can specify --invalid.

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

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.

umitools has two requirements: pysam and editdist. Use pip to install pysam.

pip install pysam

editdist has to be downloaded and installed from source (Downloads page).

wget https://py-editdist.googlecode.com/files/py-editdist-0.3.tar.gz
tar xzf py-editdist-0.3.tar.gz
cd py-editdist-0.3/
python setup.py install

Finally download and install umitools from source.

wget -O umitools-master.zip https://github.com/brwnj/umitools/archive/master.zip
unzip umitools-master.zip
cd umitools-master
python setup.py install