aaftf - 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 / fcsgx tools for cleaning contamination - polish step now more general with POLCA preferred over PILON (default) - **fixtbl** 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 https://github.com/stajichlab/AAFTF/pull/23
• Update environment.yml with pip depend by @hyphaltip in https://github.com/stajichlab/AAFTF/pull/24
• Add citation to README.md by @hyphaltip in https://github.com/stajichlab/AAFTF/pull/31
• V0.6.0 by @hyphaltip in https://github.com/stajichlab/AAFTF/pull/43

Full Changelog: https://github.com/stajichlab/AAFTF/compare/v0.4.1...v0.6.0-alpha1

- Python
Published by hyphaltip 6 months ago

aaftf - v0.4.1 release

Small documentation fix and fix pypi package problem

- Python
Published by hyphaltip about 3 years ago

aaftf - 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

- Python
Published by hyphaltip about 3 years ago

aaftf - Release v0.3.4

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

- Python
Published by hyphaltip over 3 years ago

aaftf - Release 0.3.2.1

Fixes a bug in version number. Release 0.3.2

- Python
Published by hyphaltip almost 4 years ago

aaftf - 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

- Python
Published by hyphaltip almost 4 years ago

aaftf - 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.

- Python
Published by hyphaltip almost 4 years ago

aaftf - 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

- Python
Published by hyphaltip about 4 years ago

aaftf - 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.

- Python
Published by hyphaltip almost 5 years ago

aaftf - 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

- Python
Published by hyphaltip almost 5 years ago

aaftf - v0.2.3 release with bugfixes for restarting spades runs

Support restart of pipeline after stopped - will continue SPAdes run properly.

- Python
Published by hyphaltip over 6 years ago

aaftf - Bugfix Release v0.2.2

Fix small typo in sourpurge pipeline step which had indent/space problem.

- Python
Published by hyphaltip over 7 years ago

aaftf - AAFTF release v0.2.1

Small update to v0.2.0 to update README and test_pipeline.sh to reflect new syntax. Also bump release to get Zenodo in sync.

- Python
Published by hyphaltip over 7 years ago

aaftf - AAFTF release v0.2.0

This release reworks the workdir concept, requires specification of file prefix, and switches to BBTools bbduk for trimming and filtering instead for performance and accuracy improvements.

New command 'pipeline' will generate commands of all steps at once to support pipelining.

This version has been stably run on several hundred fungal genomes in testing and production. Some memory usage tweaking has to be made (see --mem for assembly and filter steps) depending on depth of coverage and genome size.

- Python
Published by hyphaltip over 7 years ago

aaftf - Initial release archive

Make a release for initial sharing

- Python
Published by hyphaltip over 7 years ago