Dominik R Laetsch

Blobtools only parses the BAM file ... see [here](https://blobtools.readme.io/docs/coverage-parsing) for a approximate description how it works (actually done via pysam now, but should be the same filters than samtools output)...

Hi both, this is how coverage parsing works: https://blobtools.readme.io/docs/coverage-parsing#1-bam-files So i would assume that the difference is due to reads that map in supplementary/secondary alignments cheers, dom

Is the accession file a TSV?

Hi Lamm-a, sorry, i don't understand the question. please elaborate. cheers, dom

`blobtools` just takes information about sequences (length, GC, sequence similarity, coverage, ...) and aggregates it for each sequence. > I mean that why does Blobtools operate via detecting comtamination in...

Hi Gina, that is weird. Are you sure you are running python3? cheers, dom

if you post `../out1.kinfin_results/cluster_counts_by_taxon.txt` i can take a look... re `./generate_network.py` ... from the headers it looks like your files are CSVs instead of TSVs ... could that be?

I made some changes which *might* have fixed it, but I can't tell with only 10 lines ... you let me know if the issue persists and with more lines...