Denovo_Preprocessor For Preparing Solid Reads For Assembly Through Velvet_De

Question

[lin.barnum]

Hi,

The workflow for assembly of solid reads through velvet says that they need to go through a denovo_preprocessor to convert them to double encoded form. Where can I download that program? It doesn't seem to be available on the velvet site.

Thanks.

Answer 1

[Istvan Albert]

Double encoding is simply transforming: 0123 -> ATGC your could use something like:

$ tr '0123.' 'ATGCN' < data.csfasta  > double.fa

There is a short tutorial on colorspace data: http://www.biostars.org/post/show/43855/transforming-and-manipulating-color-space-reads/

[lin.barnum]

This https://banana-slug.soe.ucsc.edu/bioinformatic_tools:velvet#color-space seems to say something more than just double-encoding is going on. Also, do you trim the first two bases or not since the first base is in base space and the second base depends on the first base.

[Istvan Albert]

You are correct in that the velvet tool requires more processing than just double encoding. As it turns out I found the last published version of the tool that you are looking for on one of our computers:

http://bcc.bx.psu.edu/download/solid_denovo_preprocessor_v1.2.pl

random musing: isn't it tragic that a company that sold hundreds of sequencers each costing hundreds of thousands of dollars is allowed to fully abandon the software site that should serve the needs of the researchers using their platform ... The magnitude of abandonment is to the point where they even let the domain name http://www.solidsoftwaretools.com/ expire so that today is has an unrelated use...

[lin.barnum]

Many thanks, I was just not able to locate it anywhere. It is quite annoying the way ABI has abandoned SOLiD related tools. When I needed saet I managed to find it in an old bioscope install. Again, saet can't be found anywhere online. Even worse, solidsoftwaretools.com seems to not have been archived by archive.org either so you can't go back and find any software. Also, most Google results still seem to point to that site.

[Istvan Albert]

Yes other people have asked for SAET tool. Well, we'll provide a mirror from now on http://www.biostars.org/post/show/52250/solid-software-tools-denovo-assembly-pipeline-mirrored-at-biostar/

[lin.barnum]

This is incredibly useful. Would you also have solid_denovo_postprocessor.pl?

[Istvan Albert]

I do recall this program but only vaguely. I think that in this second version of the pipeline it has been replaced by ASiD:

The color-to base translation step is moved into ASiD and the implementation is corrected to make this step accurate and no-time consuming