GCAtools

Graph Complexity Analysis tools

Requirement

GNU Parallel

MAFFT

muscle

vg

PanPA

BubbleGun

gfatools

Useage

$ GCAtools.sh -h
GCAtools
Usage: GCAtools -f <clusterfolder> [options]

Description:
  Core workflow of GCAtools

Options:
  -h         Show this message and exit
  -f <dir>   Folder of cluster files
  -t <str>   Type of cluster files (dna or pep) [default dna]
  -d <dir>   Output file in <dir> [default ./GCAout]
  -s         Set super5 module for muscle [default False]
  -n <int>   Number of threads [default 36]

Author: Yumin Huang; ymhuang@fafu.edu.cn

$ GCAtools_prepare.sh -h
Tool:  GCAtools prepare
Usage: GCAtools_prepare -g <gff3 file> -f <genome file> [options]

Description:
  Prepare gene clusters for input

Options:
  -h Show this message and exit
  -g <string> gff3 file
  -f <string> genome fasta file
  -c <string> cds fasta file [default False]
  -p <string> pep fasta file [default False]
  -d <string> output dir [default ./results]
  -o <string> output prefix [default out]

  -m <int> minimal cluster size [default 2]

Author: Yumin Huang; ymhuang@fafu.edu.cn