v0.6.0 alpha1 release

An alpha release of 0.6.0

• fixes some problems with versions of samtools, now v1.X or v.0.X release (though v1.X is preferred for best functionality)
• supports ncbi fcs / fcs_gx tools for cleaning contamination
• polish step now more general with POLCA preferred over PILON (default)
• fix_tbl support some easy annotation (.tbl file) updates when adaptor purging occurs at 5' or 3' end of a contig
• additional changes in CHANGES.md

Things needed before a stable release

• update documentation and README for better install and usage instructions
• validation of pipeline steps which have drifted in their implementation

What's Changed

• Feature fcs gx purge by @hyphaltip in #23
• Update environment.yml with pip depend by @hyphaltip in #24
• Add citation to README.md by @hyphaltip in #31
• V0.6.0 by @hyphaltip in #43

Full Changelog: v0.4.1...v0.6.0-alpha1

v0.4.1 release

Small documentation fix and fix pypi package problem

Release v0.4.0

In this release we now report number of Telomeres recovered from Contigs in the assess sub-tool. Default monomer TAA[C]+ is searched but custom regex can be passed in. assess can also take gzip compressed FastA files as input without needing to uncompress the file.

Example assess report now looks like this after running AAFTF assess -i genome.fasta:

   CONTIG COUNT  =  189
   TOTAL LENGTH  =  19885575
            MIN  =  506
            MAX  =  1594688
         MEDIAN  =  4971
           MEAN  =  105214.68
            L50  =  12
            N50  =  536033
            L90  =  45
            N90  =  93073
            GC%  =  60.57
  T2T SCAFFOLDS  =  1
   TELOMERE FWD  =  7
   TELOMERE REV  =  17

Release v0.3.4

• fix bug #19 for an errant space in pipeline step

Release 0.3.2.1

Fixes a bug in version number.
Release 0.3.2

Release 0.3.2

This release fixes

• In assemble; Support --isolate and --careful option; --careful is default (as was in previous versions)
• updates environment.yml and requirements.txt to indicate additional packages needed

Release v0.3.1 bugfixes and enhancements

This release fixes bug in spelling of novoplasty, adds fastp options for trimming and merging reads, support for assembly/spades to run with unpaired + paired data.

There are now more extensive example of testing runs in the test folder. Future releases will sync conda/pypi installs and documentation additions.

v0.3.0 release supporting MT assembly targets

• Addresses some improvements to unique temporary dir names
• Still uses default sourmash older DB for genbank
• updates some options for pilon and running MT assembly on reads which map MT hits; working with novoplasty use --reference option to specify a reference MT genome to seed alignments

Still needed beyond this release

• additional documentation and test cases to demonstrate
• Additional polishing step support

Fix typo in v0.2.5

This is bugfix release updating v0.2.5 and should be used instead - it corrects a small typo fix.

Fixes for pilon memory and update assess report

Changelog

Release version 0.2.5

This release addresses some small additions by adding extra cmdline options to pilon (--mem) and assemble (--tmpdir).

Features/Fixes Added

• Issue #10 added GC% in the assessment report table
• Added --mem option to pilon to up the heapsize for java runs
• merged changes in namespace by @gamcil and a tmpdir