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Releases: gbouras13/dnaapler

v1.1.0

13 Jan 03:57
02bc62f
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  • Adds support for reorienting contigs where the gene of interest spands the contig ends #90. Thanks @marade @oschwengers.
  • Specifically, this is done by rotating each contig in the input by half the genome length, then running MMseqs2 for both the original and rotated contigs. The MMseqs2 hit with the highest bitscore across the original and rotated contigs will be chosen as the top hit to rotate by, therefore enabling detection of partial hits (on the original contig) that span the contig ends.
  • This has only been implemented for dnaapler all (this should be the command used by 99% of users).

v1.0.1

22 Nov 04:05
97f2ad0
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  • Thanks to the inimitable @rrwick , v1.0.1 is a patch fixing a string-parsing bug.
  • If your contig headers were integers, dnaapler did not rotate the found BLAST/MMseqs2 hits. This was a pre-existing issue (not introduced by v1.0.0).

v 1.0.0

20 Nov 23:22
4846797
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  • BREAKING CHANGE - dnaapler now uses MMseqs2 v13.45111 rather than BLAST. You will need to install MMseqs2 if you upgrade (if you use conda, it should be handled for you). The CLI is identical.
  • There are 2 reasons for this:
    1. Users reported problems installing BLAST on MacOS with Apple Silicon (see e.g. here). MMseqs2 works on all platforms and is dilligently maintained.
    2. MMseqs2 is much much faster than BLAST (what took BLAST a few minutes takes MMseqs2 seconds). We probably should have written dnaapler with MMseqs2 to begin with. MMSeqs2 v13.45111 was chosen specifically to ensure interoperability with pharokka
  • The alignment results may not be identicial to dnaapler v0.8.1 (i.e. they might find different top hits), but the actual reorientation is likely to be identical (at least in my tests). Please reach out or make an issue if you notice any discrepancies

For example - on my machine (Ubuntu 20.04, Intel i9 13th gen 13900 CPU with 32 threads), for a Staphylococcus aureus genome with 1 small plasmid, dnaapler -i staph.fasta -o staph_dnaapler -t 8 took ~129 seconds wallclock with v0.8.1 using BLAST, while it took ~3 seconds wallclock with v1.0.0 using MMseqs2.

v0.8.1

16 Sep 04:55
dfacd12
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Minor release - adds --db dnaa,repa,cog1474 as an option for dnaapler all to allow for archaea reorientation with hybracter's next version

v0.8.0

24 Jul 04:16
8484a4d
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  • Adds dnaapler archaea and adds archaeal reorientation functionality into dnaapler all - thanks @richardstoeckl
  • Specifically, this uses 403 COG1474 genes COG1474
  • Relaxes (to warning) where no BLAST hits are found - pipeline will still complete (requested in a number of issues #74 #76 #77 )

v0.7.0

06 Feb 00:55
ea07689
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  • Adds -c/--custom_db with dnaapler all to allow specifying custom databases with dnaapler all.

v 0.6.0

01 Feb 01:51
3bdd28a
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  • Fixes bug where if the starting gene (dnaA/terL/repA) was on the reverse strand, and the top BLAST hit did not find the start codon, it would reorient the genome to begin at the end of the starting gene, not the start as desired i.e. the terL would be the last gene in the output, not the first. Thanks @susiegriggo

v0.5.2

24 Jan 05:06
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  • Updates dnaapler citation and documentation to include the JOSS citation

v0.5.1

09 Jan 03:09
de745d1
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  • With dnaapler all, adds the reoriented gene to the header (thanks @ammaraziz #67 )
  • Adds --db parameter to dnaapler all allowing specifying a subset of genes to make up the database. In particular, if you have bacteria and plasmids, --db dnaa,repa should speed up Dnaapler's runtime quite a bit (thanks @oschwengers #63 )

v0.5.0

02 Dec 13:58
a9257f4
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v0.5.0 is the JOSS Release, as published in the Journal of Open-Source Software.

Add some changes with error and logging, and other minor improvements.