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This release works around some edge cases in unusual sequence libraries
and changes the behaviour of the read length module when run with the
--nogroup option. Other minor fixes are also present.

@s-andrews s-andrews released this Jan 10, 2018 · 10 commits to master since this release

Assets 2

This is a bugfix release for a bug introduced in 0.11.6. Specifically
this version would crash if the first sequence in a file was <12bp
(or less than the length of the longest adapter if a custom adapters
file was being used).

@s-andrews s-andrews released this Dec 21, 2017 · 14 commits to master since this release

Assets 2


This update fixes some bugs and updates some of the functionality to
accommodate changes in some of the sequencing platforms.

There is one major change which is that by default we now disable the
kmer module. With the inclusion of the adapter plot the value of the
information in the Kmer plot is often not great, and it is easy to
confound it if there are any over-represented sequences, or primer
compositional bias. Overall therefore we consider it best to not
routinely include this module.

If you want to turn this module back on, then simply edit the
limits.txt file in the Configuration folder of the FastQC installation
and change the line near the top which says:

kmer ignore 1

kmer ignore 0

..and the module will be re-enabled.

Other changes in this release are:

  1. Fixed a bug which prematurely abandoned the adapter content plot when long custom adapters were being used.

  2. Changed the cutoff for the maximum number of tiles to allow for the novaseq which has lots of them.

  3. Fixed a bug in the parsing of tile numbers on some illumina sequencers

  4. Added some new Clontech sequences to the contaminants list.

  5. Made the --nanopore option work with the new multi-folder ONT folder structure

  6. Added an option to specify a file name when streaming data into FastQC

  7. Added new RDF paths to check for fastq data in nanopore fast5 files

  8. Fix parsing of newer nanopore base names to correctly collate sequences

  9. Fixed a typo in the documentation for the per tile plot documentation

  10. Added a --min-length option to ignore short sequences making it easier to generate directly comparable statistics between runs.