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NGLess: NGS Processing with Less Work

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

For questions, you can also use the ngless mailing list.

Note

If you are using NGLess for generating results in a scientific publication, please cite

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 bioRxiv 367755; https://doi.org/10.1101/367755

NG-meta-profiler

For metagenomics profiling, consider using ng-meta-profiler, which is a collection of predefined pipelines developed using NGLess.

NGLess

NGLess is best illustrated by an example:

ngless "0.8"
input = paired('ctrl1.fq', 'ctrl2.fq', singles='ctrl-singles.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})

Building and installing

See the install page for more information.

Basic functionality

  • preprocessing and quality control of FastQ files
  • mapping to a reference genome (implemented through bwa by default)
  • assembly of contigs
  • annotation and summarization of the alignments using reference gene annotations
  • much more

Ngless has builtin support for model organisms:

  1. Homo sapiens (hg19)
  2. Mus Muscullus (mm10)
  3. Rattus norvegicus (rn4)
  4. Bos taurus (bosTau4)
  5. Canis familiaris (canFam2)
  6. Drosophila melanogaster (dm3)
  7. Caenorhabditis elegans (ce10)
  8. Saccharomyces cerevisiae (sacCer3)

and the standard library includes support for mOTUs, metagenomics profiling of marine samples and human gut microbiome samples. We also have standard library modules for helping users upgrading from MOCAT or running many samples (we have used NGLess on projects with >10,000 samples).

NGLess puts a strong emphasis on reproducibility.

Traditional Unix command line usage

ngless can be used as a traditional command line transformer utility, using the -e argument to pass an inline script on the command line.

The -p (or --print-last) argument tells ngless to output the value of the last expression to stdout.

Converting a SAM file to a FASTQ file

Extract file reads from a SAM (or BAM) file:

$ ngless -pe 'as_reads(samfile("file.sam"))' > file.fq

This is equivalent to the full script:

ngless "0.7" # <- version declaration, optional on the command line
samcontents = samfile("file.sam") # <- load a SAM/BAM file
reads = as_reads(samcontents) # <- just get the reads (w quality scores)
write(reads, ofname=STDOUT) # <- write them to STDOUT (default format: FASTQ)

This only works if the data in the samfile is single ended as we pipe out a single FQ file. Otherwise, you can always do:

ngless "0.7"
write(as_read(samfile("file.sam")),
        ofile="output.fq")

which will write 3 files: output.1.fq, output.2.fq, and output.singles.fq (the first two for the paired-end reads and the last one for reads without a mate).

Getting aligned reads from a SAM file as FASTQ file

Building on the previous example. We can add a select() call to only output unmapped reads:

$ ngless -pe 'as_reads(select(samfile("file.sam"), keep_if=[{mapped}]))' > file.fq

This is equivalent to the full script:

ngless "0.7" # <- version declaration, optional on the command line
samcontents = samfile("file.sam") # <- load a SAM/BAM file
samcontents = select(samcontents, keep_if=[{mapped}]) # <- select only *mapped* reads
reads = as_reads(samcontents) # <- just get the reads (w quality scores)
write(reads, ofname=STDOUT) # <- write them to STDOUT (default format: FASTQ)

Reading from STDIN

For a true Unix-like utility, the input should be read from standard input. This can be achieved with the special file STDIN. So the previous example now reads

$ cat file.sam | ngless -pe 'as_reads(select(samfile(STDIN), keep_if=[{mapped}]))' > file.fq

Obviously, this example would more interesting if the input were to come from another programme (not just cat).

Full documentation

Frequently Asked Questions (FAQ)

Authors

.. toctree::
   :hidden:
   :maxdepth: 2

   introduction
   install
   ng-meta-profiler
   whatsnew
   tutorial-ocean-metagenomics
   tutorial-assembly-gp
   tutorial-gut-metagenomics
   command-line-options
   command-line-wrappers
   one-liners
   preprocess
   Functions
   methods
   stdlib
   modules
   constants
   Organisms
   motus
   configuration
   searchpath
   reproducible
   faq
   nglesspy
   cwl
   advanced
   Language
   Mapping
   software