JohnVollmers

error trying to use coverage info from a table

4

Hi, as a test of principle I wanted to check how rosella performs on a set of contigs with absolute equal coverage values for only a single sample (basically trying...

please consider not setting default number of threads to all available cpus

1

Setting all default number of threads to "all available cores" can be a terrible policy that can wreak chaos on public servers (you can never rely on users actualy reading...

CDS-extractor.pl should return error message (and exit code 1) when no CDS could be extracted

2

When genbanks are used as input that still have windows/dos line-endings, cds-extractor.pl just quits without an error message, giving the impression that it successfully extracted all CDS. Maybe it could...

necessary fields for "-f" not stated correctly in documentation, and also not given by "--arb-list-fields"?

1

Until now, I was still struggling to get the lca classification when running sina locally. Now, using the newest version on bioconda (v1.7.1), I still could not get it to...

options for linkage information or mapped reads?

2

Since coverM is meant to replace bamm, are there any comparable options/workflows for getting contig-linkage information or to extract all reads that map to specific contigs?

Error during compilation

3

Hello, I am trying to Install Ray locally, but the compilation aborts with an error message. I cloned the most recent github-repository and tried to compile it with this make...

When extracting mapped reads from a bam file, bamm preserves information on read partners between groups by adding a prefix with that information to the extracted read-id. While this feature...

highly contaminated bins should get a warning not to use filtered data even after cleaning

1

mdmcleaner is NOT designed to rescue terrible bins. It is only meant to validate good quality and to make good bins better! This needs to be reflected in the results,...

simplify report tables

1

currently the output tables are a bit convoluted and not user friendly. Instead of outputing the infos "as is", digest them a bit more to be better readable