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.
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})
Cabal version 1.18 or higher is necessary.
Running make should build a sandbox and download/install all dependencies
into it.
- Luis Pedro Coelho (email: coelho@embl.de) (on twitter: @luispedrocoelho)
- Paulo Monteiro
- Ana Teresa Freitas