CoverM

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Hi and hope all is well! I just wanted to jump in and leave a quick recommendation for documentation. Specifically that I think CoverM lacks any real-life example walkthroughs with...

erfanshekarriz

What is the formula for function "Mean"

1

Appreciate the development of this great tool. For the function Mean, I am a little bit confused about the formula. I would assume it is mainly based on total mapped...

Harper19

How change the path of tmp files

1

Hi developers, I would like to know how to change the path where intermediate files are stored during the execution of CoverM. Due to limited personal tmp storage space on...

microbial-cookie

Hi, when I run 'coverm contig' with many samples, it always takes so much time. So I would like to know whther I can use Intermediate file to calculate some...

PonderLi

Hi, Thanks for the tool. Could you please consider supporing [strobealign](https://github.com/ksahlin/strobealign) as a mapper option. It has both the aligner and mapping functions - similar to minimap2 - and can...

PoisonAlien

defining an output file

7

Hi all, I have difficulty defining an output file for my relative abundance run, any hints please what am I missing here? ``` coverm genome --genome-fasta-extension fasta --genome-fasta-files *.fa \...

Sabrin2020

Failed to correctly find or parse BAM file at "/tmp/coverm_fifo.tDWtDjcZrfy4/foo.pipe"

1

Hello, I was using coverm to calculate the reads count mapped to a few genomes. But i frequently met the following probelm. Would you please help me to take a...

Hollyhlp

Hi, dear developers: Thanks for great work! I just wonder if it's more accurate to set --exclude-supplementart when calculating rpkm or tpm? I noticed that you said coverm use supplementary...

PonderLi

``` + Arg::new("dereplication-cluster-method") + .long("dereplication-cluster-method") + .value_parser(["fastani", "skani"]) + .default_value(galah::DEFAULT_CLUSTER_METHOD), ``` Don't hard-code in coverm, but refer to galah's

wwood

bam_generator] Failed to correctly find or parse BAM file at "/tmp/coverm_fifo.wyqhN9T2ujOl/foo.pipe"

5

When using coverM, I met the following problem. May I know how to solve it? Thank you. 2022-08-02T06:51:55Z INFO coverm::mapping_index_maintenance] Generating BWA_MEM index for /tmp/.tmpzfBZeD .. [2022-08-02T07:14:01Z INFO coverm::mapping_index_maintenance] Finished...

Hollyhlp