What’s New (History)

IN DEVELOPMENT

Support for minimap2 as alternative mapper. Import the minimap2 module and specify the mapper when calling map. For example:

ngless '0.7'
import "minimap2" version "1.0"

input = paired('sample.1.fq', 'sample.2.fq', singles='sample.singles.fq')
mapped = map(input, fafile='ref.fna', mapper='minimap2')
write(mapped, ofile='output.sam')

Internal improvements

Version 0.7.1

Released Mar 17 2018

Improves memory usage in count() and the use the when-true flag in external modules.

Version 0.7

Released Mar 7 2018

New functionality in NGLess language

  • Added max_trim argument to filter method of MappedReadSet.
  • Support saving compressed SAM files
  • Support for saving interleaved FastQ files
  • Compute number Basepairs in FastQ stats
  • Add headers argument to samfile function

Bug fixes

  • Fix count’s mode {intersection_strict} to no longer behave as {union}
  • Fix as_reads() for single-end reads
  • Fix select() corner case

In addition, this release also improves both speed and memory usage.

Version 0.6

Released Nov 29 2017

Behavioural changes

  • Changed include_m1 default in count() function to True

New functionality in NGLess language

  • Added orf_find function (implemented through Prodigal) for open reading frame (ORF) predition
  • Add qcstats() function to retrieve the computed QC stats.
  • Added reference alias for a more human readable name
  • Updated builtin referenced to include latest releases of assemblies

New functionality in NGLess tools

  • Add –index-path functionality to define where to write indices.
  • Allow citations as key in external modules (generally better citations information)
  • Use multiple threads in SAM->BAM conversion
  • Better error checking/script validation

Bug fixes

  • Output preprocessed FQ statistics (had been erroneously removed)
  • Fix –strict-threads command-line option spelling
  • Version embedded megahit binary
  • Fixed inconsistency between reference identifiers and underlying files

Version 0.5.1

Released Nov 2 2017

Fixed some build issues

Version 0.5

Released Nov 1 2017

First release supporting all basic functionality.