CoverM

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[Feature Request] Add a method to calculate genome coverage (e.g., 1X, 10X, 100X)

3

I'm submitting a bunch of genomes to NCBI and they want genome coverage: >The estimated base coverage across the genome, eg 12x. This can be calculated by dividing the number...

jolespin

PacBio and Illumina FASTQ Files - one coverage from multiple input files

3

### Discussed in https://github.com/wwood/CoverM/discussions/120 Originally posted by **kevinmyers** June 28, 2022 I have a set of 217 MAGs that I would like to use coverM to determine the overall coverage...

wwood

ERROR coverm::genomes_and_contigs he contig 'k141_142388_length_1308_cov_6.0000' has been assigned to multiple genomes, at least 'JL17_bin.20' and 'WA23_bin.33'

1

[2022-03-16T05:03:15Z INFO coverm] CoverM version 0.6.1 [2022-03-16T05:03:15Z INFO coverm] Writing output to file: /lustre/home/liutang/41groundwater/14host/01MAGs/05host_abundance/host_rpkm.tsv [2022-03-16T05:03:15Z INFO coverm] Using min-covered-fraction 10% [2022-03-16T05:03:15Z INFO coverm] Using min-read-percent-identity 95% [2022-03-16T05:03:15Z INFO coverm] Using...

ZongzhiWu

multi-threading CoverM coverage estimation via data parallelism library rayon

7

Dear Ben, I saw that in genome.rs line 147: per_genome_coverage_estimators[genome_index].iter_mut() we can use rayon::preclude::*; in Cargo.toml and replace .iter_mut() with par_inter_mut(), everything else should be exactly the same including map...

jianshu93

Hi Ben, I just wanted to get your thoughts on whether you think the other three metrics that use contig length should be doing what the `mean` calculation is. Specifically,...

jeffkimbrel

Hi, this is more of a question than an issue. I apologize if it's been asked before (I searched but didn't see much). Are the mapping algorithms set up to...

mcmahon-uw

Dear Ben, I am wondering whether there could be a tabular format output like the PAF format after or before filtering bam files, which can be used for plotting. I...

jianshu93

Meaning of the totalAvgDepth column in the metabat method

1

Hi Ben, Thanks for writing CoverM, I find it very useful. So far I have been using jgi_summarize_bam_contig_depths but I suspect it contains some bugs, including inconsistencies in coverage calculation...

CK7

Option to produce percent identity summary

1

Hello, I have been using CoverM often for filtering my BAM files based on read percent identity. I am wondering if there is any possibility of adding an option to...

edgraham

Dear Ben, I am wondering whether we can also add a recruitment plot option to coverm genome module. It is always important to check the coverage of each contigs and...

jianshu93