Ngless is a domain-specific language for NGS (next-generation sequencing data) processing.

Example

ngless "1.0"
input = fastq(['ctrl2.fq','ctrl2.fq','stim1.fq','stim2.fq'])
input = preprocess(input) using |read|:
    read = read[5:]
    read = substrim(read, min_quality=26)
    if len(read) < 31:
        discard

mapped = map(input, reference='hg19')
write(count(mapped, features=['gene']),
        ofile='gene_counts.csv',
        format={csv})

More information: https://ngless.embl.de.