Parameters

Table of contents

  1. anno
  2. generator
  3. mkref
  4. evaluate
  5. refine
  7. identity
  8. General parameters
  9. Decomposition parameters
  10. Annotation parameters
  11. Output parameters

anno

generator

mkref

evaluate

refine

identity

I/O Options: input FASTA file you want to annotate output output prefix

General parameters

parameters description default
-c, –config CONFIG config file in JSON, CONFLICT with –AUTO None
-t, –thread THREAD number of threads 1
–AUTO automatically estimate parameters False
–debug output running time of each module and alignments False
-w, –window-length parallel window size 5000
-o, –overlap-length windows overlap size 1000
-r, –resource memory limit (GB) 50

Decomposition parameters

parameters description default
-k, –ksize k-mer size for building De Bruijn graph 5
-m, –motif reference motif set path None
-n, –motifnum maximum number of motifs 30
–abud-threshold min threshold campared with top edge weight 0.01
–abud-min min edge weight in De Bruijn graph 3
–plot paint De bruijn graph for each windows False
–no-denovo not de novo find motifs, use reference motifs to annotate False

Annotation parameters

parameters description default
–force add reference motifs into annotation False
–annotation-dist-ratio max distance to map 0.4
–finding-dist-ratio max distance to query in reference motif set 0.4
–match-score score per matched base 1
–lendif-penalty hope that mapped sequence is as long as the motif 0.01
–gap-penalty penalty per skipped base 1
–distance_penalty penalty per distance 1.5
–perfect-bonus bonus per matched base if there is no difference in alignment 0.5

Output parameters

parameters description default
–quiet don’t output thread completion informing False
–file minimum output score 5
-s, –score minimum output score 5