Dedumi deduplicates read sets from paired end sequencing based on the Unique Molecular Identifiers (UMIs) ligated to the start of each read. Deduplication is based on the uniqueness of the UMIs, with some additional bases for genomic context, with only the first read encountered output.
This project has Nix expressions provided for
building and developing. To build with nix, run nix build, and to
drop into a development shell use nix develop.
The project can also be built using hpack and cabal. First
generate a cabal file with hpack and then build the binary with
cabal build.
Run dedumi --help for some brief explanation of the parameters. The
input and output are paired end fastq files, so an example invocation
(with default parameters) is:
dedumi input_R{1,2}.fastq.gz output_R{1,2}.fastq.gz
The output will then contain the deduplicated reads with UMIs stripped from each read pair.
- umiLength: The number of bases at the start of each read corresponding to the UMI
- extraHashBases: Additional bases following the UMI to use as genetic context
- filterSize: The size of the Cuckoo filter. If the filter reaches capacity this can be increased. Lowering the capacity reduces memory consumption.