montoias / ngless

NGLess: NGS with less work

NGLess: NGS Processing with Less Work

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

Note: This is pre-release software, currently available as a preview only. Please get in touch if you want to use it in your work.

Example

ngless "0.0"
input = fastq(['ctrl1.fq','ctrl2.fq','stim1.fq','stim2.fq'])
preprocess(input) using |read|:
    read = read[5:]
    read = substrim(read, min_quality=26)
    if len(read) < 31:
        discard

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

Dependencies

Cabal version 1.18 or higher is necessary.

Running make should build a sandbox and download/install all dependencies into it.

More information

• Full documentation
• Frequently Asked Questions (FAQ)
• ngless webpage

Authors

• Luis Pedro Coelho (email: [email protected]) (on twitter: @luispedrocoelho)
• Paulo Monteiro
• Ana Teresa Freitas