Awesome

Getting Started

git clone https://github.com/lh3/gfaview
cd gfaview
make
wget https://github.com/lh3/gfaview/releases/download/data/miniasm-ecoli.gfa.gz
./gfaview -rtbom miniasm-ecoli.gfa.gz > transformed.gfa

Introduction

This repo implements a command-line tool as well as a library in C that parses, validates and transforms assembly graphs in a dialect of the GFA1 format, which is loosely defined by the following grammar:

<id?>     ::= /[!-~]+/
<ori?>    ::= /[+-]/
<seq>     ::= /[!-~]+|\*/
<cigar>   ::= /([0-9]+[MIDSN])+/
<tag>     ::= /[A-Za-z][A-Za-z0-9_]:[ifAZB]:[ -~]+/
<olen?>   ::= /[0-9]+/

<format>  ::= ( <segment> | <link> )+
<segment> ::= S <id> <seq> <tag>*
<link>    ::= L <id1> <ori1> <id2> <ori2> <overlap> <tag>*
<overlap> ::= <olen> | <olen1>:<olen2> | <cigar>

The gfa-chk.l file gives the more precise regular grammar that parses the format. In comparison to the original GFA format, this dialect allows to describe overlaps with one or two overlap lengths. For example, an overlap 50:51 indicates a 50bp suffix of the first segment in the link overlaps with a 51bp prefix of the second segment. An overlap 50 is a shorthand of 50:50 or equivalently 50M. The new overlap field is essential to long-read overlaps as overlappers often do not output detailed CIGAR.

The command-line tool, gfaview, parses input graph and more importantly checks its integrity. It discards segments with unknown lengths (e.g. segments used on L-lines but not defined on S-lines), identifies duplicated links (when two links have the same starting/ending vertices and the same overlap lengths), and fills in missing information (e.g. for an overlap field like 50: or :51; missing S-lines but with inferrable segment lengths) as much as possible. Gfaview outputs a correctly formatted GFA1 that is usually easier to parse. Gfaview may also optionally apply a series of transformations such as subsetting, tip trimming, bubble popping, short overlap purging and unitigging. These operations are ported from miniasm and focus on long-read assembly for now.