fastp

Fastp

Location: Github

Install

## get source (you can also use browser to download from master or releases)
git clone https://github.com/OpenGene/fastp.git
## build
cd fastp
make
## Install
sudo make install

Just download the build version:

wget http://opengene.org/fastp/fastp
chmod a+x fastp

Bioconda

conda install -c bioconda fastp

Usage

fastp -i in.fq -o out.fq
## for paired end data (gzip compressed)
fastp -i in.R1.fq.gz -I in.R2.fq.gz -o out.R1.fq.gz -O out.R2.fq.gz

Some Examples

delete reads with mean score value >= 20

• To remove reads with a mean quality score lower than 20 using fastp, you can use the -e option. This option sets the minimum mean quality score required for a read to be kept. If the mean quality score of a read is below this threshold, the read will be discarded.
  
• for single end: fastp -i input.fq -o filtered_output.fq -e 20
  
• for paired-ends: fastp -i in1.fq -I in2.fq -o out1.fq -O out2.fq -e 20