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RELEASE_NOTES.md

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Release notes for AAFTF

Automatic Assembly For The Fungi

  • v0.4.0

    1. linted code better with flake8
    2. Support gzipped assembly files in assess
    3. Add telomere counting to assess

  • v0.3.3

    1. Created pypi packaging now

  • v0.3.2

    1. In assemble; Support --isolate and --careful option; --careful is default (as was in previous versions)

  • v0.3.1

    1. Support novoplasty Mitochondria targeted assembly runs with the AAFTF mito option uses either default seed assembly (A.nidulans) or you can specify your own target
    2. Support for alternative sourpurge databases - gtdb (r207) and gtdb-rep (r207) along with default 2018 genbank-k31 release which still p erforms generally best
    3. trimming supports fastp now with support for de-duplication option; merged option to merge paired end overlapping reads; and additional novoseq/NextSeq trailing 'G' option trimming; support for fastp in trimming (trim) command which can now support merging (--merge) and de-duplication (--dedup) as well as 5' and 3' trimming options of fastp (--cutfront, --cuttail, --cutright).
    4. fix bug in mito to correctly spell novoplasty program that is used
    5. revamped the resources.py to allow multiple files to represent mitochondria ref db for vector screening and alternative sourmash LCA databases - supporting gtdb-r207 and gtdb-rep-r207
    6. spades in assemble command support merged long singleton reads along with paired end input
    7. added tests and summary stats to compare performance of different trimming/merging strategies on final genome and gene content

  • v0.3.0

    1. added novoplasty and mito sub-command
    2. better support for downloading sourmash lca db if it doesn't exist

  • v0.2.4

    1. conda/pypi packages

  • v0.2.3

    1. support a minimum length contig cutoff

  • v0.2.1

    1. Fix some README docs
    2. Sync zenodo with this release

  • v0.2.0

    1. rework temporary file, prefix use throughout, not relying on a set working directory so that multiple runs can be completed in a single folder without clashes of names.
    2. Switch to BBTools bbduk for quality trimming instead of Trimmomatic
    3. Switch to BBTools bbduk instead of BWA/Bowtie for mapping to contamination db. Speed improvements and accuracy of kmer matches to contamination over alignment-based cleanup.
    4. Specify memory use for pilon, spades assembly steps
    5. Support to generate scripts to run all steps in a pipeline with 'pipeline' cmd

  • v0.1.0

    1. Initial release which includes automation for quality trimming and contaminant/adaptor removal, filtering, assembly, veccleanup, refinement, and duplication removal and sorting