gfa tools is a set of tools for manipulating sequence graphs in the GFA or the
rGFA format. It has implemented parsing, subgraph and conversion to FASTA/BED.
More functionality may be added in future.
Location and version:
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$ which gfatools
/local/cluster/bin/gfatools
$ gfatools version
gfa.h: 0.5-r234
gfatools: 0.4-r214-dirty
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help message:
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$ gfatools
Usage: gfatools <command> <arguments>
Commands:
view read a GFA file
stat statistics about a GFA file
gfa2fa convert GFA to FASTA
gfa2bed convert rGFA to BED (requiring rGFA)
blacklist blacklist regions
bubble print bubble-like regions (EXPERIMENTAL)
asm miniasm-like graph transformation
sql export rGFA to SQLite (requiring rGFA)
version print version number
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software ref: https://github.com/lh3/gfatools/
research ref: