agtools Command-Line Interface Reference

agtools provides a software framework for manipulating assembly graphs.

Run agtools --help or agtools -h to display the main help message.

Usage: agtools [OPTIONS] COMMAND [ARGS]...

  agtools: A Software Framework to Manipulate Assembly Graphs

Options:
  -v, --version  Show the version and exit.
  -h, --help     Show this message and exit.

Commands:
  stats      Compute statistics about the graph
  rename     Rename segments, paths and walks in a GFA file
  concat     Concatenate two or more GFA files
  filter     Filter segments from GFA file
  clean      Clean a GFA file based on segments in a FASTA file
  component  Extract a component containing a given segment
  fastg2gfa  Convert FASTG file to GFA format
  gfa2fastg  Convert GFA file to FASTG format
  asqg2gfa   Convert ASQG file to GFA format
  gfa2asqg   Convert GFA file to ASQG format
  gfa2dot    Convert GFA file to DOT format (GraphViz)
  gfa2fasta  Get segments in FASTA format
  gfa2adj    Get adjacency matrix of the assembly graph

`stats`

Compute statistics about the graph.

Run agtools stats --help or agtools stats -h to list the help message.

Usage: agtools stats [OPTIONS]

  Compute statistics about the graph

Options:
  -g, --graph PATH      path(s) to the assembly graph file(s)  [required]
  -o, --output FILE     path to the output file  [required]
  -lf, --log-file FILE  optional path to write output logs; by default no log
                        file is created
  -h, --help            Show this message and exit.

Inputs

Assembly graph file in GFA format

Outputs

Text file containing graph statistics

`rename`

Rename segments, paths and walks in a GFA file.

Run agtools rename --help or agtools rename -h to list the help message.

Usage: agtools rename [OPTIONS]

  Rename segments, paths and walks in a GFA file

Options:
  -g, --graph PATH      path(s) to the assembly graph file(s)  [required]
  -p, --prefix TEXT     prefix for the graph elements  [default: ""]
  -o, --output FILE     path to the output file  [required]
  -lf, --log-file FILE  optional path to write output logs; by default no log
                        file is created
  -h, --help            Show this message and exit.

Inputs

Assembly graph file in GFA format
Prefix to prepend to segments, paths, and walks

Outputs

Assembly graph file in GFA format with renamed elements

`concat`

Concatenate two or more GFA files.

Run agtools concat --help or agtools concat -h to list the help message.

Usage: agtools concat [OPTIONS]

  Concatenate two or more GFA files

Options:
  -g, --graph PATH      path(s) to the assembly graph file(s)  [required]
  -o, --output FILE     path to the output file  [required]
  -lf, --log-file FILE  optional path to write output logs; by default no log
                        file is created
  -h, --help            Show this message and exit.

Inputs

Multiple assembly graph files in GFA format. You can provide each file followed by -g.

Outputs

A concatenated assembly graph file in GFA format

`filter`

Filter segments from a GFA file based on length.

Run agtools filter --help or agtools filter -h to list the help message.

Usage: agtools filter [OPTIONS]

  Filter segments from GFA file

Options:
  -g, --graph PATH          path(s) to the assembly graph file(s)  [required]
  -l, --min-length INTEGER  minimum length of segments to keep  [default: 100;
                            required]
  -o, --output FILE         path to the output file  [required]
  -lf, --log-file FILE      optional path to write output logs; by default no
                            log file is created
  -h, --help                Show this message and exit.

Inputs

Assembly graph file in GFA format
Minimum length of segments to keep

Outputs

Filtered assembly graph file in GFA format

`clean`

Clean a GFA file based on segments in a FASTA file.

Run agtools clean --help or agtools clean -h to list the help message.

Usage: agtools clean [OPTIONS]

  Clean a GFA file based on segments in a FASTA file

Options:
  -g, --graph PATH      path(s) to the assembly graph file(s)  [required]
  -f, --fasta PATH      path to the FASTA file  [required]
  -a, --assembler TEXT  assembler name (if assembler used is myloasm)
  -o, --output FILE     path to the output file  [required]
  -lf, --log-file FILE  optional path to write output logs; by default no log
                        file is created
  -h, --help            Show this message and exit.

Inputs

Assembly graph file in GFA format
FASTA file with segment sequences
Name of the assembler (if applicable)

Outputs

Cleaned assembly graph file in GFA format. Removes segments that are not found in the FASTA file and adds sequences if they are not present in the GFA file (to be compatible with the GFA specification).

`component`

Extract a component containing a given segment.

Run agtools component --help or agtools component -h to list the help message.

Usage: agtools component [OPTIONS]

  Extract a component containing a given segment

Options:
  -g, --graph PATH      path(s) to the assembly graph file(s)  [required]
  -s, --segment TEXT    segment ID  [required]
  -o, --output FILE     path to the output file  [required]
  -lf, --log-file FILE  optional path to write output logs; by default no log
                        file is created
  -h, --help            Show this message and exit.

Inputs

Assembly graph file in GFA format
Segment ID of interest

Outputs

Assembly graph file of the corresponding component in GFA format

`fastg2gfa`

Convert a FASTG file to GFA format.

Run agtools fastg2gfa --help or agtools fastg2gfa -h to list the help message.

Usage: agtools fastg2gfa [OPTIONS]

  Convert FASTG file to GFA format

Options:
  -g, --graph PATH      path(s) to the assembly graph file(s)  [required]
  -k, --ksize INTEGER   k-mer size used for the assembly  [default: 141;
                        required]
  -o, --output FILE     path to the output file  [required]
  -lf, --log-file FILE  optional path to write output logs; by default no log
                        file is created
  -h, --help            Show this message and exit.

Inputs

Assembly graph file in FASTG format
k-mer size used for the assembly

Outputs

Assembly graph file in GFA format

`gfa2fastg`

Convert a GFA file to FASTG format.

Run agtools gfa2fastg --help or agtools gfa2fastg -h to list the help message.

Usage: agtools gfa2fastg [OPTIONS]

  Convert GFA file to FASTG format

Options:
  -g, --graph PATH      path(s) to the assembly graph file(s)  [required]
  -o, --output FILE     path to the output file  [required]
  -lf, --log-file FILE  optional path to write output logs; by default no log
                        file is created
  -h, --help            Show this message and exit.

Inputs

Assembly graph file in GFA format

Outputs

Assembly graph file in FASTG format

`asqg2gfa`

Convert an ASQG file to GFA format.

Run agtools asqg2gfa --help or agtools asqg2gfa -h to list the help message.

Usage: agtools asqg2gfa [OPTIONS]

  Convert ASQG file to GFA format

Options:
  -g, --graph PATH      path(s) to the assembly graph file(s)  [required]
  -o, --output FILE     path to the output file  [required]
  -lf, --log-file FILE  optional path to write output logs; by default no log
                        file is created
  -h, --help            Show this message and exit.

Inputs

Assembly graph file in ASQG format

Outputs

Assembly graph file in GFA format

`gfa2asqg`

Convert a GFA file to ASQG format.

Run agtools gfa2asqg --help or agtools gfa2asqg -h to list the help message.

Usage: agtools gfa2asqg [OPTIONS]

  Convert GFA file to ASQG format

Options:
  -g, --graph PATH      path(s) to the assembly graph file(s)  [required]
  -o, --output FILE     path to the output file  [required]
  -lf, --log-file FILE  optional path to write output logs; by default no log
                        file is created
  -h, --help            Show this message and exit.

Inputs

Assembly graph file in GFA format

Outputs

Assembly graph file in ASQG format

`gfa2dot`

Convert a GFA file to GraphViz DOT format or ABySS DOT format.

Run agtools gfa2dot --help or agtools gfa2dot -h to list the help message.

Usage: agtools gfa2dot [OPTIONS]

  Convert GFA file to DOT format (GraphViz)

Options:
  -g, --graph PATH      path(s) to the assembly graph file(s)  [required]
  -ab, --abyss          use the ABySS DOT format for the output
  -o, --output FILE     path to the output file  [required]
  -lf, --log-file FILE  optional path to write output logs; by default no log
                        file is created
  -h, --help            Show this message and exit.

Inputs

Assembly graph file in GFA format

Outputs

Assembly graph file in GraphViz DOT format or ABySS DOT format.

`gfa2fasta`

Get segments from a GFA file in FASTA format.

Run agtools gfa2fasta --help or agtools gfa2fasta -h to list the help message.

Usage: agtools gfa2fasta [OPTIONS]

  Get segments in FASTA format

Options:
  -g, --graph PATH      path(s) to the assembly graph file(s)  [required]
  -o, --output FILE     path to the output file  [required]
  -lf, --log-file FILE  optional path to write output logs; by default no log
                        file is created
  -h, --help            Show this message and exit.

Inputs

Assembly graph file in GFA format

Outputs

Segment sequences in FASTA format

`gfa2adj`

Get the adjacency matrix of the assembly graph.

Run agtools gfa2adj --help or agtools gfa2adj -h to list the help message.

Usage: agtools gfa2adj [OPTIONS]

  Get adjacency matrix of the assembly graph

Options:
  -g, --graph PATH         path(s) to the assembly graph file(s)  [required]
  --delimiter [comma|tab]  delimiter for adjacency file. Supports a comma and
                           a tab.  [default: comma]
  -o, --output FILE        path to the output file  [required]
  -lf, --log-file FILE     optional path to write output logs; by default no
                           log file is created
  -h, --help               Show this message and exit.

Inputs

Assembly graph file in GFA format

Outputs

A delimited file of the adjacency matrix