CoverM
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wwood
Read coverage calculator for metagenomics
Hi, I am currently running `coverm genome` to estimate the abundance of multiple viral genomes in my samples. However I am not sure which is the best way to do...
Hello! This is a bit of a strange request, but I am running into a strange error when running dockerized versions of CoverM. It is related to [this](https://discussion.fedoraproject.org/t/where-is-the-which-command-defined/62701) somehow, I...
Hi, thank you for the wonderful tool. Can coverM be used for assessing genomes or MAGs proportion in metatranscriptomics reads? I guess it might be the normalization of reads prior...
Hello, I would like to check the coverage difference before and after trimmed_mean. Currently I am thinking to create depth table and plots using old vs new bamfiles to check....
Hi Ben, I'm trying to run coverm contig with the --sharded flag, but it appears to generate some issues which is difficult to comprehend. My current command is: coverm contig...
Hi, all What does this parameter mean "--min-read-percent-identity ", when I use the command to calculate the bam's RPKM, I found that different "--min-read-percent-identity" are different, when 99, bam file...
Dear CoverM team, I remember I suggested skani some time ago, and glad to see you included it in the newest version. However, you might notice inaccuracy estimations below 85%...
CoverM is useful to caculate the abundance of genomes. However, I am confused about the output of coverm. Here are to command line that I have tried before (one with...
Hi! I wanted to point out that running ```coverm contig --coupled ....``` with 40+ samples doesn't scale well when compared to running each sample individually and then merging the output...
Hi! Is there a way to filter output based on minimum horizontal coverage? To validate that the reads covered most of the genome (instead of one part if the MAGs...
