wwood/CoverM

Issues

• Calculating RPKM of metaT reads against a collection of MAGs

  #230 opened 2 months ago by EMagadur
  4

• Build fails on i386: error[E0308]: mismatched types

  #227 opened 2 months ago by yurivict
  2

• Increasing number of genomes increases relative abundance of all genomes?

  #208 opened 10 months ago by lxsteiner
  5

• What is the formula for function "Mean"

  #191 opened 2 months ago by Harper19
  1

• coverm seems only used the forward reads

  #194 opened 2 months ago by quliping
  5

• How to output bam file after trimmed_mean function?

  #206 opened 2 months ago by Harper19
  2

• Request -- use https://crates.io/crates/which for external command checking?

  #207 opened 2 months ago by nickp60
  7

• Question abount the genome module of coverm

  #215 opened 2 months ago by quliping
  1

• Add coverM to homebrew-bio

  #228 opened 3 months ago by jianshu93
  0

• need help

  #223 opened 3 months ago by XRL-1343959526
  1

• Filtering by MapQ

  #219 opened 4 months ago by SDmetagenomics
  3

• Discussion/request: Read extraction for multiple references

  #220 opened 4 months ago by strejcem
  1

• pay attention to skani accuracy below 85% ANI

  #199 opened a year ago by jianshu93
  4

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

  #217 opened 6 months ago by brilliant2643
  2

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

  #211 opened 8 months ago by microjishuai
  1

• compressed fasta input

  #218 opened 6 months ago by jvollme
  2

• cryptic error when running coverM genome

  #216 opened 7 months ago by nixon444
  4

• Support for strobealign

  #186 opened 7 months ago by PoisonAlien
  1

• Question about the bam file

  #212 opened 8 months ago by jiaojiaoguan
  4

• Estimating the abundances of multiple viral genomes

  #210 opened 9 months ago by asierFernandezP
  5

• Mean coverage calculation

  #209 opened 9 months ago by ramiroricardo
  2

• CoverM to assess genomes relative proportion in Metatranscriptomics data?

  #167 opened 2 years ago by JSSaini
  1

• Error when using sharded flag

  #205 opened 10 months ago by AvriXue
  0

• Error: fastANI executable not found despite being installed

  #204 opened 10 months ago by xzzhouxi
  2

• What is the meaning about "--min-read-percent-identity "

  #189 opened a year ago by weiguanyue
  1

• [Enhancement] Improving Multi-sample Parallelisation Strategy

  #193 opened a year ago by erfanshekarriz
  2

• How to cite CoverM

  #176 opened a year ago by SarahIsme
  2

• Filter based on minimum horizontal coverage

  #195 opened a year ago by ntromas
  2

• Best measurement for conducting differential abundance analysis

  #177 opened a year ago by Somebodyatthdoor
  8

• [Documentation] Example tutorial walkthroughs and test data

  #192 opened a year ago by erfanshekarriz
  0

• How change the path of tmp files

  #190 opened a year ago by microbial-cookie
  1

• bwa, bwa-mem, or bwa-mem2?

  #188 opened a year ago by rfox-mbl
  1

• coverm contig Intermediate file

  #187 opened a year ago by PonderLi
  0

• libtinfow.so.6: no version information available (required by samtools)

  #170 opened 2 years ago by bhimbbiswa
  2

• ERROR coverm::bam_generator

  #185 opened a year ago by jamesriddellv
  4

• defining an output file

  #184 opened a year ago by Sabrin2020
  7

• tpm and --exclude-supplementary

  #183 opened a year ago by PonderLi
  0

• A question about rpkm

  #179 opened a year ago by LRH1995
  11

• Error: There are no found reference sequences that are a part of a genome

  #182 opened a year ago by vmkhot
  2

• clarity on min-covered-fraction

  #178 opened a year ago by itsmisterbrown
  2

• An error during the installation of development version

  #181 opened a year ago by ilnamkang
  4

• paper cut: define clsuter methods possibilities properly

  #180 opened a year ago by wwood
  0

• How can I provide extra parameters to BWA using the "--bwa-params" option?

  #168 opened a year ago by ilnamkang
  3

• Extracting bam files

  #166 opened a year ago by ntromas
  1

• default rep seq picking method

  #173 opened a year ago by itsmisterbrown
  2

• thread 'main' panicked at 'index out of bounds: the len is 6564 but the index is 6586'

  #175 opened 2 years ago by haleyhallowell
  4

• Unable to find BAM file when file exists

  #174 opened 2 years ago by iwilkie
  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 opened 2 years ago by JiaLonghao1997
  3

• Usage of --sharded

  #172 opened 2 years ago by Rridley7
  0

• Q: coverM compatible with bowtie2

  #171 opened 2 years ago by aistBMRG
  1