News:Solid Software Tools: Denovo Assembly/Xsq Tools Pipeline Mirrored At Biostar

Question

[Istvan Albert]

The Solid Software Tools website seems to have been abandoned by the vendor and the software that used to be hosted on the site is now unavailable. We decided to provide a mirror for the content originally distributed from that site starting with DeNovo Assembly Pipeline version 2.

Downloads can be accessed at http://www.biostars.org/static/downloads/solid/

DeNovo Assembly Pipeline

• DeNovo_Assembly_Pipeline_2.0.pdf
• DeNovoAssemblyProtocol0060810.pdf
• SOLiD™ Accuracy Enhancement Tool
• Assembly Assistant for SOLiD
• Color space utilities: such as solid_denovo_preprocessor_v1.2.pl, miniAssembler.jar and others
• Download the full archive: solid-denovo-assembly.tar.gz

XSQ Tools

XSQ is a proprietary data format produced by the SOLiD instrument. It is a binary compressed format based on HDF5. The XSQ scripts from this package can transform this format into text csfasta and qual formats.

• XSQ Tools User Guide
• Download the full distribution: xsq.tools.tar.gz

Solid2SRF

Program to Convert SOLiD Sequencing reads (CSFASTA) to NCBI's SRF format

The original developer of these tools has contacted us with information to a “unofficial, but authorized” project on github to release code and binaries for these utilities.

https://github.com/solidsoftwaretools/solid2srf

If you have access to other tools that used to be hosted on the Solid Software Tools website please contact us at [e-mail].

[Leandro de Mattos]

Dear, all, I I discovered why the error looking for code assemble.pl.It was because I had not compiled the program asid.1.0. In the manual does not talk about it, only about velvet and mummer.

Who persists always reaches :D :D

Thanks anyway.

Mattoslmp

[Istvan Albert]

thanks for following up on it

[lin.barnum]

This is really useful.

[Istvan Albert]

Thanks to Mario Deng for submitting the XSQ Tools package

[Leandro de Mattos]

Hi I ran the program assemble.pl in the sample directory with the command:

perl assemble.pl ./f3.csfasta ./f3.qual 20000 -r3 ./r3.csfasta -r3qv ./r3.qual -ins_length 1300 -ins_length_sd 400

And getting the output:

[0.121196] Writing into graph file assembly/velvet/LastGraph...
Final graph has 95 nodes and n50 of 10883, max 18909, total 41961, using 6046/8998 reads
Running Assisted Assembly for SOLiD
/media/mattos/29b2a202-8bd3-44a1-858a-b83a294f113a/home/mattos/RNAseq_solid_analiser/F3/denovo2/asid.1.0/asid_light -collect assembly/velvet/LastGraph assembly/velvet/contigs.fa assembly/velvet/Sequences 1300 assembly/postprocessor/gap_reads
Contigs merging failed when extracting gap reads.

So, at the end of the process occurred some problem, someone has any suggestions which can have occurred.

Thanks in advance for any help,

Leandro

[Istvan Albert]

This is not a traditional forum, new questions should be asked at top level and not as followups to other posts. Very few people read old posts to answer them.

Answer 1

[zainab12khanum]

Hello,

Please can you tell me about the short read allignment assemblers for RNA seq using XSQ FORMAT.

Thank you.