Do vecscreen and sourpurge have similar functions? about aaftf HOT 6 CLOSED

yes

• filter is for reads uses BBMap by default against a contamination and primer/adaptor database. It can also be given a set of accessions to screen against if you have known contamination you want to remove at the read level.
• vecscreen is for assembled contigs - this is probably going to be replaced with the ncbi fcs-adaptor step - it recapitulated a vector screening tool that was at ncbi online https://www.ncbi.nlm.nih.gov/tools/vecscreen/ - this step will remove parts or whole contigs that match a vector and adaptor database - if a vector match is found within a contig the contig is split into pieces since one cannot be sure the linkage of the contig is sound now.
• sourpurge is looking for cross-species contamination and removes the entire contig if it is classified as contamination. this is may be subsituted with ncbi fcs-gx

from aaftf.

Vecscreen removes primer and obvious contam (phiX) and trims
Or splits contigs using univec db.

Sourpurge screens scaffolds for contamination by looking for matches to groups outside the phylum. It removes scaffolds that are likely matching to a contamination source.

I have also just written in support for NCBI fcs-Gx tool which does similar thing to sourmash/sourpurge step.

from aaftf.

In addition to vecscreen and sourpurge, the filter function is also involved in removing gene fragments of non-target species. The filter step removes reads before the assemble step, and also removes reads of mitochondrial genes from the mito step. Therefore, in AAFTF, there are three steps involved in removing gene fragments of non-target species.

Did I summarize it correctly?

from aaftf.

someday soon I'll finish writing up a manuscript on the tool to give this more description.

the ncbi fcs-adapator and fcs-gx are being tested but gx is a little unwieldy as it needs a lot of memory and large DB while sourpurge is pretty small footprint (though the version of the DB I had been using before was removed from OSF.io so the default install may not work right now till we see if the replacement larger DB can still work efficiently).

from aaftf.

fcs-gx support is now in AAFTF - available in live code and will be part of the v0.5.0 release

from aaftf.

0.5.0 has these features. closing this query since answered above.

from aaftf.