Adjacency Files For Abyss-Explorer

Question

[2184687-1231-83-]

Hi,

Where can I find example input files for abyss-explorer? Is the format specified somewhere?

[Michael]

Hi, if you want answers to this question you should provide more instant information on the topic. This will also make this question useful to others, which it now definitely is not. What is abyss/ abyss-explorer? (It's a rather novel transcriptome assembler) http://www.ncbi.nlm.nih.gov/pubmed/19834150

Did you ask the authors: [e-mail], [e-mail] , ask them first, what did they answer?

I looked at the pages, seems like both programs are very poorly documented at first glance. Ask the authors for additional documentation, maybe.

Answer 1

[Rob Syme]

On the ABySS-Explorer project page, there are links to two example data sets, a Human BAC clone assembly and an E.coli genome assembly.

The files that you need from your assembly are the adjacency file (.adj), the contigs (.fasta) and the distance file (.dist).

These files need to be in the same directory, and it's easiest to simply open them where they lie in the assembly folder.