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


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