wwood CoverM issues - Githubissues

wwood / CoverM

Read coverage calculator for metagenomics

GNU General Public License v3.0

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How can I use CoverM to calculate the abundace of hybrid-assembly recovered MAGs?

#217 brilliant2643 opened 2 days ago
0
cryptic error when running coverM genome

#216 nixon444 opened 1 week ago
3
Question abount the genome module of coverm

#215 quliping opened 3 weeks ago
1
add strobealign to mappers in help

#214 AroneyS closed 2 weeks ago
3
Fix covered_fraction help

#213 AroneyS closed 1 month ago
1
Question about the bam file

#212 jiaojiaoguan closed 1 month ago
4
"relative_abundance" option was not provided in "contig" mode

#211 microjishuai opened 1 month ago
0
Estimating the abundances of multiple viral genomes

#210 asierFernandezP opened 2 months ago
5
Mean coverage calculation

#209 ramiroricardo closed 2 months ago
2
Increasing number of genomes increases relative abundance of all genomes?

#208 lxsteiner closed 3 months ago
4
Request -- use https://crates.io/crates/which for external command checking?

#207 nickp60 opened 3 months ago
3
How to output bam file after trimmed_mean function?

#206 Harper19 opened 3 months ago
2
Error when using sharded flag

#205 AvriXue opened 3 months ago
0
Error: fastANI executable not found despite being installed

#204 xzzhouxi closed 3 months ago
2
feat: use equality for xnor operation on booleans

#203 lavafroth closed 4 months ago
1
refactor: pass inexpensive `f32` instead of `&f32`

#202 lavafroth closed 4 months ago
1
tests: replace manual file reads with fs::read_to_string

#201 lavafroth closed 4 months ago
1
refactor: use iterator's position method to find first index of occurrence

#200 lavafroth closed 5 months ago
1
pay attention to skani accuracy below 85% ANI

#199 jianshu93 opened 5 months ago
3
Add doi to citation

#198 AroneyS closed 5 months ago
0
Add release script

#197 AroneyS closed 5 months ago
0
add citation

#196 AroneyS closed 5 months ago
7
Filter based on minimum horizontal coverage

#195 ntromas opened 5 months ago
2
coverm seems only used the forward reads

#194 quliping opened 6 months ago
5
[Enhancement] Improving Multi-sample Parallelisation Strategy

#193 erfanshekarriz opened 6 months ago
2
[Documentation] Example tutorial walkthroughs and test data

#192 erfanshekarriz opened 6 months ago
0
What is the formula for function "Mean"

#191 Harper19 opened 6 months ago
1
How change the path of tmp files

#190 microbial-cookie opened 6 months ago
1
What is the meaning about "--min-read-percent-identity "

#189 weiguanyue opened 7 months ago
1
bwa, bwa-mem, or bwa-mem2?

#188 rfox-mbl closed 7 months ago
1
coverm contig Intermediate file

#187 PonderLi opened 7 months ago
0
Support for strobealign

#186 PoisonAlien closed 2 weeks ago
1
ERROR coverm::bam_generator

#185 jamesriddellv closed 9 months ago
4
defining an output file

#184 Sabrin2020 opened 10 months ago
7
tpm and --exclude-supplementary

#183 PonderLi opened 10 months ago
0
Error: There are no found reference sequences that are a part of a genome

#182 vmkhot closed 10 months ago
2
An error during the installation of development version

#181 ilnamkang closed 10 months ago
4
paper cut: define clsuter methods possibilities properly

#180 wwood opened 10 months ago
0
A question about rpkm

#179 LRH1995 closed 10 months ago
11
clarity on min-covered-fraction

#178 itsmisterbrown closed 10 months ago
2
Best measurement for conducting differential abundance analysis

#177 Somebodyatthdoor closed 10 months ago
8
How to cite CoverM

#176 SarahIsme closed 5 months ago
2
thread 'main' panicked at 'index out of bounds: the len is 6564 but the index is 6586'

#175 haleyhallowell closed 11 months ago
4
Unable to find BAM file when file exists

#174 iwilkie closed 11 months ago
2
default rep seq picking method

#173 itsmisterbrown closed 10 months ago
2
Usage of --sharded

#172 Rridley7 opened 1 year ago
0
Q: coverM compatible with bowtie2

#171 aistBMRG closed 1 year ago
1
libtinfow.so.6: no version information available (required by samtools)

#170 bhimbbiswa closed 1 year ago
2
[2023-06-04T07:45:16Z INFO coverm::contig] In sample 'cdhit_rep_seq.fna/SRR13083091_1.fq.gz', found 0 reads mapped out of 0 total (NaN%)

#169 JiaLonghao1997 opened 1 year ago
3
How can I provide extra parameters to BWA using the "--bwa-params" option?

#168 ilnamkang closed 10 months ago
3