NGLess

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

NGLess 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})

NGLess links

• NGLess documentation
• NGLess Github repository
• NGLess manuscript: NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language by Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork in Microbiome 2019