CoverM

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Sharded flag not respected when calculating contig coverage

1

Hi Ben, I'm trying to run `coverm contig` with the `--sharded` flag, but it appears CoverM still expects the BAM files to be reference sorted: ``` > samtools sort -n...

donovan-h-parks

Hi, Thanks for the cool pipeline! I wonder if there is a way to count (and/or remove) the reads that map to multiple locations. I've seen that option (--exclude-supplementary) but...

ntromas

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?

jvollme

``` $ cargo run -- contig -m metabat -b tests/data/issue_19_bams/*bam --no-zeros Finished dev [unoptimized + debuginfo] target(s) in 0.07s Running `target/debug/coverm contig -m metabat -b tests/data/issue_19_bams/BE_BS_R1-BE_BS_R1.reduced.bam tests/data/issue_19_bams/BE_BS_R1-BE_RX_R1.reduced.bam tests/data/issue_19_bams/BE_BS_R1-BM_ER_R7.reduced.bam tests/data/issue_19_bams/BE_BS_R1-BM_RX_R7.reduced.bam --no-zeros`...

wwood

Filtering by MapQ

2

Would it be possible to add an option to filter read alignments by mapQ score? This can be useful for metagenomics datasets where many similar organisms are being compared.

SDmetagenomics

"relative_abundance" option was not provided in "contig" mode

1

Hi Ben, The "contig" mode doesn't provide "relative_abundance" option for coverage measures. Could you please explain the reasons for this setting? What are your concerns about calculating the relative abundance...

microjishuai

Question abount the genome module of coverm

1

Hello, coverm is a good software and very helpful for my work. However, I'm not sure about the calculation process of the 'genome' module of CoverM. It is very easy...

quliping

Discussion/request: Read extraction for multiple references

1

Hi, I’m looking for a tool that can extract FASTQ reads mapped to multiple individual references, but specifically for long nanopore reads. Unfortunately, I haven’t been able to find any...

strejcem

Thoughts @AroneyS ? Can you please take it for a spin on some real data?

wwood