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@alneberg alneberg released this Aug 2, 2019

This release includes mostly bugfixes and stability improvements. However, one change is potentially braking: subcontigs are now labeled with the suffix .concoct_part_XX where XX is the part number. This is enforced by the core script used to create the coverage table.

For a complete list of changes, see below:

Changed

  • #236 - Always add suffix to contigs at cutup, even when they are not cut.
  • #254 - Slight cleanup of concoct refine
  • #258 - New suffices (.concoct_part_XX) are now used for contig parts
  • #261 - Epsilon argument removed as it was not working and is not very useful
  • #262 - Rewrote documentation, including installation instructions
  • #264 - concoct_part_ suffix is enforced in subcontig for coverage script
  • #264 - Header line is enforced for input for merge_cutup_clustering.py and extract_fasta_bins.py
  • #267 - Updated documentation

Added

  • #253 - A dockerfile useful to test the conda installation
  • #258 - Tests for all fundamental scripts, including a new integration test data repository
  • #259 - This changelog
  • #262 - Added documentation for the core scripts used with concoct
  • #265 - A warning is now printed when concoct runs in single threaded mode

Fixed

  • #230 - Enable at least single threaded installation on Mac OSX
  • #231 - Replace pandas .ix with .loc to fix deprecation warnings
  • #246 - Limit some dependency version numbers for python 2
  • #254 - Concoct refine now works with python 3
  • #258 - Seed tests now working again
  • #260 - Fix the dockerfile build by adding integration test data
Assets 2

@alneberg alneberg released this Dec 12, 2018 · 71 commits to master since this release

Improved Speed

  • Improved parallelism using OpenMP allowing efficient scaling to a large number of parallel threads
  • By only running one instead of ten iterations of the same algorithm, speed is improved drastically.

As an example: A test run on real data resulted in a 22x speed up on a 20 core computer, from 15hours 28min to 42min.

Improved usability

  • Now runs on both Python 2 and Python 3. - Please beware that the performance on Python 3 is slightly faster than python 2.
  • Installation through conda is now supported: conda install concoct
  • A new step concoct_refine is introduced where one can rerun the concoct algorithm on seemingly merged clusters.
  • Possible to run without rerunning mapping against cut up contigs. This improves the compatibility of concoct against other existing binning software.
Assets 2

@alneberg alneberg released this Nov 23, 2018 · 162 commits to master since this release

New minor release with some fixes to installation and hopelessly outdated documentation.

Assets 2
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