| This is a commandline utility to remove exact duplicate reads from paired-end fastq files. Reads are assumed to be in 2 separate files. Read sequences are then concatenated and a short hash is calculated on the concatenated sequence. If the hash has been previsouly seen the read will be dropped from the output file. This means that reads that have the same start and end coordinate, but differ in lengths will not be removed (but those will be "flattened" to at most 1 occurence). This algorithm is very simple and fast, and saves memory as compared to reading the whole fastq file into memory, such as fastuniq does. |
hg clone https://toolshed.g2.bx.psu.edu/repos/mvdbeek/dedup_hash
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| with fast and memory-efficient sequence hashes | 0.1.1 | any | |