Fastp

What’s it for

• A fast way to trim adapters from fastq reads.
• Also does quality filtering.
• type fastp -h for full info

Example use

fastp \
--in1 R1.fq.gz --out1 R1_trimmed.fq.gz \
--in2 R2.fq.gz --out2 R2_trimmed.fq.gz \
--failed_out fastp_fails.fq.gz \
--verbose \
--adapter_fasta adapter_seqs.fa \
--n_base_limit 5 \
--thread 16 

• default: if reads from only one set passes, both will be discarded
• default: compression level - 4
• –n_base_limit means how many Ns allowed in seq
• adapter seq mismatch is 1 per 8 bases I think
• outputs a fastp.html file with info (although adapter seqs table is truncated)

Links

• Github repo: [https://github.com/OpenGene/fastp]https://github.com/OpenGene/fastp](https://github.com/OpenGene/fastp)
• Paper: https://doi.org/10.1093/bioinformatics/bty560