Releases | Open Source Science

Dnaapler - v1.3.0

Thanks to @mbhall88 the functionality of --ignore has been extended

If your input FASTA or GFA is mixed (e.g. has chromosome and plasmids), you can also use dnaapler all, with the option to ignore some contigs with the --ignore parameter. The --ignore parameter now accepts either:

A file path containing contig names to ignore (one per line)
A comma-separated list of contig names (e.g., chr1,chr2,chr3)
to read contig names from stdin (one per line) using -

e.g.

dnaapler all -i input.fasta -o output_directory_path -p my_genome_name --ignore list_of_contigs_to_ignore.txt

dnaapler all -i input.fasta -o output_directory_path -p my_genome_name --ignore chr1,chr2,chr3

echo -e "chr1\nchr2\nchr3" | dnaapler all -i input.fasta -o output_directory_path -p my_genome_name --ignore -

Scientific Software - Peer-reviewed - Python
Published by gbouras13 9 months ago

Dnaapler - v1.2.0

Thanks to the one and only @rrwick, Dnaapler now supports the GFA format as input. This was done to ensure support for Ryan's new bacterial genome assembly tool Autocycler, the successor to Trycycler, but may also be useful if you have GFA files from e.g. Unicycler, Flye, Spades or other assemblers.
- If you run dnaapler with GFA input, you will get a GFA output as well.
- If you run dnaapler with GFA input, only circular contigs will be reoriented
Relaxes the MMSeqs2 dependency to >=13.45111

Scientific Software - Peer-reviewed - Python
Published by gbouras13 about 1 year ago

Dnaapler - v1.1.0

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).

Scientific Software - Peer-reviewed - Python
Published by gbouras13 over 1 year ago

Dnaapler - v1.0.1

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).

Scientific Software - Peer-reviewed - Python
Published by gbouras13 over 1 year ago

Dnaapler - v 1.0.0

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.

Scientific Software - Peer-reviewed - Python
Published by gbouras13 over 1 year ago

Dnaapler - v0.8.1

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

Scientific Software - Peer-reviewed - Python
Published by gbouras13 over 1 year ago

Dnaapler - v0.8.0

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 )

Scientific Software - Peer-reviewed - Python
Published by gbouras13 almost 2 years ago