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stajichlab / AAFTF

Automatic Assembly For The Fungi
MIT License
19 stars 4 forks source link

Integrate NCBI tax tool in screening #7

Open hyphaltip opened 4 years ago

hyphaltip commented 4 years ago

https://github.com/ncbi/ngs-tools/tree/tax/tools/tax tool provides way to screen for contamination in reads or contigs before processing

hyphaltip commented 2 years ago

large scale database install needed to replicate NCBI process, unclear at this point if it is that superior to sourpurge and the vecscreen logic already - there are small instances that appear when submitting genomes but it isn't clear this is useful overhead for this tool as full install of NCBI resources are very large and require dedicated machine with high memory.

hyphaltip commented 1 year ago

Add FCS-adaptor to vecscreen step -- https://github.com/ncbi/fcs/wiki/FCS-adaptor