Problems with filtering the host genome

[neokie-sun]

Dear developers,
I just wanted to say a big thank you for developing SqueezeMeta. It's a really efficient and convenient tool that's made it much easier for researchers to get their work done quickly and efficiently.
I was just wondering: when analysing mammalian gut microbiota metagenome data using SqueezeMeta (according to the following: SqueezeMeta.pl -m coassembly -p neotest -s /mnt/f/database_sequeezemeta/test/testsample.txt -f /mnt/f/database_sequeezemeta/test/raw -t 8), does it include the step of filtering the host genome?

[jtamames]

Hello
Thanks for the compliments! SqueezeMeta does not do any filtering of reads by default. You must do that yourself before providing the reads to the pipeline. You can use sqm_mapper.pl for doing it.
Best,
J

[neokie-sun]

Thank you for your reply. But I have another problem: SQMtools loading the .zip file via loadSQM is causing the R environment to crash (R session aborted). Reinstalling R or SQMtools doesn't solve the problem. R version 4.4.1.

[fpusan]

See workaround in #755