Describe the ASQG file format

jts / sga

de novo sequence assembler using string graphs

http://genome.cshlp.org/content/22/3/549

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Describe the ASQG file format #66

Closed sjackman closed 10 years ago

sjackman commented 10 years ago

Here's a relevant posting.

sjackman commented 10 years ago

The ABySS file formats wiki: https://github.com/bcgsc/abyss/wiki/ABySS-File-Formats

jts commented 10 years ago

A basic description has been added to the wiki:

https://github.com/jts/sga/wiki/ASQG-Format

sjackman commented 10 years ago

Thanks, Jared. ASQG and SAM are in many ways similar, describing an (overlap) alignment. What are the advantages of ASQG over SAM, do you think? Easier to parse the tab-delimited fields of ASQG than the CIGAR string of SAM, for sure.

jts commented 10 years ago

It is possible to represent pairwise overlaps with SAM but I don't feel its very natural. I like the simplicity of ASQG for this.

ASQG was never meant to be a public format anyway. I needed to represent a graph for SGA and the SQG/fastg discussions had not taken off yet. ASQG was meant to be temporary while a format was designed by the community. ASQG has held up relatively well but there are a few things I'd change if I could.

Vini2 commented 4 years ago

What is the idea behind a number of differences in overlap value for -1? For example, I have the following output and would like to know the correct interpretation.

ED contig-1510 contig-1658 0 289 1269 38 327 328 0 -1

Thanks