I'll start, but it won't be a complete answer. These descriptions are based on an answer from Shaun on the ABySS mailing list in Oct09
dist
DistanceEst --help
Estimate distances between contigs using paired-end alignments.
21 : | 420877,-30,47,5.5,0
39 : 125053,-30,17,9.2,1 | 10061,-30,25,7.6,1 132861,47,16,9.5,0 219341,45,15,9.8,0 294681,44,16,9.5,0 300788,43,17,9.2,0 419176,44,16,9.5,0 426650,46,15,9.8,0
110 : 44048,-30,30,6.9,0 |
170 : 397327,9,20,8.5,0 410536,23,43,5.8,1 50658,-5,11,11.4,0 | 161076,51,11,11.4,1 283551,-27,14,10.1,0 324935,-13,25,7.6,1 4522,81,10,12.0,0
171 : 298574,39,10,12.0,1 313291,-7,20,8.5,1 | 134144,22,27,7.3,1
173 : 119549,-15,59,4.9,0 129210,-30,26,7.4,1 | 181775,-11,37,6.2,1 200470,-30,13,10.5,1
- id0 : id1,distance,number-of-pairs,error,strand | id2,...
- id1 comes after id0
- id2 comes before id0
I'm not sure what it means when there are multiple sets of space-separated groups (e.g. the 170: entry)
adj
AdjList --help
Find all contigs that overlap by exactly k-1 bases.
0 [ 396267,1 ] [ 55802,0 ]
1 [ 35373,0 102691,0 ] [ 249534,0 ]
2 [ 277705,0 ] [ 350054,1 ]
3 [ 132932,0 ] [ 271245,0 182962,0 ]
- id0 length [ id1,strand ... ] [ id2,strand ... ]
- id1 comes after id0
- id2 comes before id0
overlap.fa
Overlap --help
Find overlaps between blunt contigs that have negative distance estimates. Output the small contigs that fill in the gaps.
>47 25 0 33+ 38+ -15
- id0 length coverage (always 0) id1 id2 overlap
- id1 comes before id0
- id2 comes after id0
- id1 and id2 overlap by the specified number of bases (negative distance indicates overlap)
path
SimpleGraph --help Find paths through contigs using distance estimates.
@ 19,1 -> 416835,0
@ 37,0 -> 123886,1
@ 38,0 -> 401731,1 4851,0
@ 109,0 -> 43659,0
@ 168,0 -> 50189,0 69838,0 202180,1 117665,1 393524,0 406599,1
- id0,direction -> id1,strand ...
- direction = 0: id1 comes after id0
- direction = 1: id1 comes before id0
Hi @Rob, please consider editing into a question format. As is it, your post is really a comment and it is hard to see how we can either contribute or help you here. Cheers