Remove too short reads from fastq files

Filtering fastq sequences based on read lengths

using usearch7

remove all reads shorter than 80nt

usearch7 -fastq_filter SAMPLE.fastq -fastq_minlen 80 -fastqout SAMPLE_filtered.fastq

http://www.drive5.com/usearch/manual/fastq_filter.html

using Python

fastx_len_filter.py (N. Segata Lab)

# download

wget https://bitbucket.org/nsegata/pyphlan/raw/ee5eb06/fastx_len_filter.py

using awk

http://seqanswers.com/forums/showthread.php?t=31845