SeqPurge is a highly sensitive adapter trimmer for paired-end short read data.
Using SeqPurge is pretty intuituve. This example shows the use when trimming and merging data of a sample that was sequenced on two lanes:
> SeqPurge -in1 R1_L1.fastq.gz R1_L2.fastq.gz -in2 R2_L1.fastq.gz R2_L2.fastq.gz -out1 R1.fastq.gz -out2 R2.fastq.gz
The main parameters of SeqPurge are:
- a1 - Forward read adapter sequence.
- a2 - Reverse read adapter sequence.
- mep - Maximum error probability of insert and adapter matches - this is the main parameter that balances seensitivity and specificity.
- qcut - Quality trimming cutoff.
- ncut - Number of subsequent Ns to trimmed.
SeqPurge was published as a full paper in BMC Bioinformatics.
Additionally, there is a poster presented at ECCB 2016 availiable, which contains the latest benchmarks.
The SeqPurge command-line help and changelog can be found here.