Comments (6)
Yes, actually could replace nearly all steps with bbmap.... would reduce number of dependencies. But could leave in code so that can use several aligners for example. But I've been using bbduk.sh for adapter trimming first, then phiX removal. https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/
from aaftf.
yes I think this might be best thing to do that -- are you able to share any best practices out of that?
I've got something started but maybe you can help tweak. Mainly would not do trim/filter separately.
from aaftf.
trying to think about whether this is generalizeable - in that there are a lot of options do we really want to enable pass through of those (eg a general "here's the string to pass to bbduk.sh?")
from aaftf.
I more/less used what Brian has listed as default settings -- I tend to not quality trim prior to assembly, but removal of adapters/phix required.
We could have an option to pass directly to any of these tools, but for standard illumina adapter trimming/phix removal, I can't think of a use case where I've modified anything other than minimum length to keep for example.
from aaftf.
I do need to do custom contaminant filtering - that's my heavy use case for this where we seem to have bacteria and it would be helpful to remove as much as possible before assembly instead of the megablast at the end I think (though some circularity needed).
from aaftf.
We now support BBMap (bbduk.sh) as default for screening for contaminants.
from aaftf.
Related Issues (18)
- different gunzip/gzip options on osx/linux in vecscreen.py HOT 3
- Add GC% in 'assess' command HOT 1
- After to setup of the requirements, how to install? Is it necessary a sudo user? HOT 4
- Out of Memory on default pilon run HOT 1
- Add racon as polishing step
- sourmash LCA database update url? HOT 18
- AAFTF pipeline always fails at vecscreen step HOT 2
- Support single-end and interleaved fastq data HOT 3
- [Enhancement] Assembly for Nanopore reads HOT 2
- error when running AAFTF filter and AAFTF vecscreen HOT 5
- Do vecscreen and sourpurge have similar functions? HOT 6
- masurca polca.sh breaks with recent samtools HOT 1
- AAFTF pipeline exiting when mito fails HOT 3
- Generate command list as top-level running HOT 1
- Specify version numbers of all sub-tools
- Integrate NCBI tax tool in screening HOT 2
- support other assemblers: dipspades HOT 1
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from aaftf.