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B-UMMI / INNUca

INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search
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running INNUCA for pseudomonas aeruginosa, Enterobacter cloacae and ralstonia mannitolilytica #37

Open bala-ruokavirasto opened 2 years ago

bala-ruokavirasto commented 2 years ago

Dear INNUCA team,

Is it possible to run INNUCA for other species than the one listed in the below modules?

https://github.com/B-UMMI/INNUca/tree/master/modules/trueCoverage_rematch campylobacter_jejuni.config v2.3 5 years ago campylobacter_jejuni.fasta v2.3 5 years ago combine_trueCoverage_reports.py v3.1 5 years ago escherichia_coli.config v3.1 5 years ago escherichia_coli.fasta v2.5 5 years ago haemophilus_influenzae.config Make trueCoverage executable and add references for other species 4 years ago haemophilus_influenzae.fasta Make trueCoverage executable and add references for other species 4 years ago listeria_monocytogenes.config Change Listeria monocytogenes trueCoverage defaults and sequences 4 years ago listeria_monocytogenes.fasta Properly format fasta 4 years ago salmonella_enterica.config v2.5 5 years ago salmonella_enterica.fasta v2.5 5 years ago streptococcus_agalactiae.config v2.3 5 years ago streptococcus_agalactiae.fasta v2.5 5 years ago streptococcus_dysgalactiae.config Make trueCoverage executable and add references for other species 4 years ago streptococcus_dysgalactiae.fasta Make trueCoverage executable and add references for other species 4 years ago streptococcus_pneumoniae.config Make trueCoverage executable and add references for other species 4 years ago streptococcus_pneumoniae.fasta Make trueCoverage executable and add references for other species 4 years ago streptococcus_pyogenes.config Make trueCoverage executable and add references for other species 4 years ago streptococcus_pyogenes.fasta Make trueCoverage executable and add references for other species 4 years ago yersinia_enterocolitica.config v2.3 5 years ago yersinia_enterocolitica.fasta v2.3 5 years ago

Kindly clarify what are the additional things needed to setup for analysis of pseudomonas aeruginosa, Enterobacter cloacae and ralstonia mannitolilytica species?

Best Regards, Bala

bala-ruokavirasto commented 1 year ago

Also for Enterococcus faecalis and Enterococcus faecium species.... Hope the necessary files can be added to the upcoming versions of innuca so that we can run Innuca for these species as well?

I wonder this issue is here for more than a year.. Anyone kindly reply what was the status?

Best Regards, Bala