settings_MetaPlastHunter.yaml

#################################
##     MetaPlastHunter         ##
##      settings file          ##
## Please add full paths below ##
#################################

###### Software ######

Software dependencies:

  bbduk.sh: /opt/bbmap/
  bbmap.sh: /opt/bbmap/
  pileup.sh: /opt/bbmap/
  randomreads.sh: /opt/bbmap/

#### Databases and mapping files ######

Databases and mapping files:

  bbmap_base: /home/karlicki/reference_database_no_masked_1209_new.fasta
  seqid2taxid.map: /home/karlicki/seqid2taxid.map
  silva: /home/karlicki/ribosomal_db.fa
  compressed_Silva: /home/karlicki/compressed_ribosomal_db.fa.gz
  kmers: /home/karlicki/comp_19_3.fa
  empirical_treshold: /home/karlicki/metaplasthunter_empirical_tresholds.txt

#### Params ####

Params:

  min_number_of_reads: 50
  percentile_treshold: 1
  min_bin_coverage: 0
  bincov4_report: 0
  lca_treshold: 0.00001
  static_coverage_treshold[%]: 1
  min_identity: 0.7
  bincov_len: 100

### Kmer pre-classification ###

Preliminary classification:

  minkmerhits: 1
  kmer_len: 31