v0.3.1

Fix a bug in the lca.pl script that was leading to incomplete taxonomic annotations for some ORFs.

v0.3.0

New features:

• Two new read mappers (bwa and minimap2) can be selected using the -map parameter when calling squeezeM. Minimap2 can be run in three different modes.
  -- minimap2-on: for MinION reads.
  -- minimap2-pb: for PacBio reads.
  -- minimap2-sr: for Illumina reads.
• Initial support for Oxford Nanopore MinION / PacBio reads. SqueezeM now supports the use of single-end reads. SqueezeM will treat a sample as single-end if a "pair2" is not specified for that sample in the samples file. SqueezeM now also includes an specific aligner for long reads.
• An initial implementation of the SqueezeM database and web interface can now be found in https://github.com/jtamames/SqueezeMdb.

Bug fixes:

• Fix viral taxonomy being incorrectly parsed.
• Fix a bug during database creation.

v0.2.0

New features:

• Classify the rRNA genes predicted by barrnap using the RDP classifier.
• Predict metabolic pathways for each bin using MinPath.

Bug fixes:

• Several.

v0.1.3

Initial release.