News: Solid Software Tools: Denovo Assembly/Xsq Tools Pipeline Mirrored At Biostar
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gravatar for Istvan Albert
7.1 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

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

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.

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 admin@biostars.org.

news • 5.3k views
ADD COMMENTlink modified 3.2 years ago by zainab12khanum0 • written 7.1 years ago by Istvan Albert ♦♦ 81k
2

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

 

ADD REPLYlink written 4.7 years ago by Leandro de Mattos90
1

thanks for following up on it

ADD REPLYlink written 4.7 years ago by Istvan Albert ♦♦ 81k

This is really useful.

ADD REPLYlink written 7.1 years ago by lin.barnum230

Thanks to Mario Deng for submitting the XSQ Tools package

ADD REPLYlink written 7.1 years ago by Istvan Albert ♦♦ 81k

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.

 

 

 

 

ADD REPLYlink written 4.7 years ago by Leandro de Mattos90

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.

ADD REPLYlink written 4.7 years ago by Istvan Albert ♦♦ 81k
0
gravatar for zainab12khanum
3.2 years ago by
International Center for Chemical and Biological Sciences
zainab12khanum0 wrote:

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

ADD COMMENTlink written 3.2 years ago by zainab12khanum0
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