snayfach/IGGsearch

Issues

• Default value for min_sp_quality

  #32 opened 5 months ago by jannemm
  1

• is it SAM/BAM format? Consider opening with check_sq=False

  #28 opened 6 years ago by nbutyrate
  4

• Bug in merge?

  #31 opened 5 years ago by Javelarb
  3

• Make possible to install using pip or conda

  #30 opened 5 years ago by boulund
  2

• custom database

  #29 opened 5 years ago by alienzj
  1

• Peak RAM

  #20 opened 6 years ago by snayfach
  0

• check for existence of input files

  #19 opened 6 years ago by snayfach
  0

• Support for BIOM format

  #8 opened 6 years ago by snayfach
  0

• Paired end reads

  #6 opened 6 years ago by snayfach
  0

• Evaluate USCMGs

  #15 opened 6 years ago by snayfach
  0

• Update README

  #16 opened 6 years ago by snayfach
  0

• Comparison to MIDAS

  #27 opened 6 years ago by durrantmm
  1

• customized database of species-specific marker genes

  #26 opened 6 years ago by yejunbin
  1

• allow user to supply list of markers or species to exclude

  #22 opened 6 years ago by snayfach
  1

• add license

  #21 opened 6 years ago by snayfach
  0

• add .gitignore

  #23 opened 6 years ago by snayfach
  0

• remove old files

  #24 opened 6 years ago by snayfach
  0

• Add option to exclude species based on genome-quality

  #11 opened 6 years ago by snayfach
  0

• Provide full database and gut-only database

  #10 opened 6 years ago by snayfach
  0

• Add taxonomy information

  #7 opened 6 years ago by snayfach
  0

• Species names

  #5 opened 6 years ago by snayfach
  0

• Option to report all species or only detected species

  #14 opened 6 years ago by snayfach
  1

• Add support for FASTA

  #17 opened 6 years ago by snayfach
  1

• RuntimeWarning: Mean of empty slice.

  #18 opened 6 years ago by snayfach
  0

• Support for bowtie2

  #9 opened 6 years ago by snayfach
  0

• —min_intra_freq (using 0.1, 0.5, 0.9 yielded same results)

  #3 opened 6 years ago by zjshi
  0

• —mapid (works; may use narrower value range, e.g. 50 and 1 have same results)

  #4 opened 6 years ago by zjshi
  0

• Add description and default values in help text for -w, —min_intra_freq and --max_inter_freq flag

  #2 opened 6 years ago by zjshi
  0

• Report total # of % of reads mapped, # of species detected

  #12 opened 6 years ago by snayfach
  0

• Add presence/absence information to output file

  #13 opened 6 years ago by snayfach
  0

• Add taxonomic info to the output

  #1 opened 6 years ago by zjshi
  1