Question: Abyss Output File Formats
3
gravatar for Rob Syme
8.9 years ago by
Rob Syme530
Perth, Western Australia
Rob Syme530 wrote:

There are a series of output files produced by ABYSS that describe how the contigs and scaffolds were constructed. The types of files seems to differ from version to version, so I thought it would be great to have an exhaustive list of the file format definitions. Files that people I've seen include:

  • .adj
  • .dist
  • .path
  • .pair
  • overlap.fa

What data do these files contain, and what format do they take?

assembly format • 5.4k views
ADD COMMENTlink modified 8.1 years ago by virajbdeshpande0 • written 8.9 years ago by Rob Syme530

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

ADD REPLYlink written 8.6 years ago by Eric Normandeau10k
3
gravatar for Rob Syme
8.9 years ago by
Rob Syme530
Perth, Western Australia
Rob Syme530 wrote:

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
ADD COMMENTlink modified 5 months ago by RamRS20k • written 8.9 years ago by Rob Syme530
0
gravatar for Madalina
7.5 years ago by
Madalina0
Madalina0 wrote:

how did obtain those files? because when I run ABySS, I obtain only the contig file?

ADD COMMENTlink written 7.5 years ago by Madalina0

This question was based on an older version of ABySS. The newer versions have different outputs. I'll probably end up deleting this entry to save future confusion.

ADD REPLYlink written 7.5 years ago by Rob Syme530
0
gravatar for Kaushik
7.4 years ago by
Kaushik0
Kaushik0 wrote:

The above explained files are obtained when we provide paired end files

ADD COMMENTlink written 7.4 years ago by Kaushik0
0
gravatar for virajbdeshpande
6.8 years ago by
virajbdeshpande0 wrote:

Here are my guesses after I tried to look at the source code:

.adj files overlapindex length coverage(total count of mapping base-pairs) ; contigs connected to head [-d overlap size] ; contigs connected to tail

I do not know what is the convention for head and tail or +/- end.

ADD COMMENTlink written 6.8 years ago by virajbdeshpande0
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