ngs_backbone

[Jose Blanca]

Hi:

We have created a tool to analyze NGS sequences and we think that it might be of some interest f
or some of the seqanswers members. We are using this tool in non model species to:
- clean sanger, 454 and illumina sequences,
- assemble transcriptomes (using mira),
- map reads to a reference genome,
- call SNPs and indels,
- filter SNPs and,
- annotate sequences (descriptions, GO terms, SSRs, etc.)

This software is written in python and released under the aGPL licence. Right now we consider it
beta software and although we're using it in several of our projects you can find some rough ed
ges when using the initial release. You can find more information at the ngs_backbone site.

If you try it out we would like to hear from you.

Best regards,

Jose Blanca

[tt.tom]

dear sir/madam
I have use the backbone_analysis.py -a prepare_mira_assembly
backbone_analysis.py -a mira_assembly
And I found there is nothing in the /home/ngs_user/ngs_workshop/maize/assembly/20111115_0204/result dir,the dir like this:
---------------------------------------------------------------
ngs_user@ngsmachine:~/ngs_workshop/maize$ ls -l
total 24
drwxr-xr-x 4 ngs_user ngs_user 4096 2011-11-15 03:04 assembly
-rw------- 1 ngs_user ngs_user 4311 2011-11-14 09:51 backbone.conf
-rw-r--r-- 1 ngs_user ngs_user 3778 2011-11-15 03:04 backbone.log
drwxr-xr-x 4 ngs_user ngs_user 4096 2011-11-14 09:51 reads
drwxr-xr-x 2 ngs_user ngs_user 4096 2011-11-15 03:04 tmp
------------------------------------------------------------------------
and the assembly dir like this:
ngs_user@ngsmachine:~/ngs_workshop/maize/assembly$ ls -l
total 8
drwxr-xr-x 3 ngs_user ngs_user 4096 2011-11-15 03:04 20111115_0204
drwxr-xr-x 2 ngs_user ngs_user 4096 2011-11-14 09:59 input
--------------------------------------------------------------------------
and the input dir like this:
gs_user@ngsmachine:~/ngs_workshop/maize/assembly/input$ ls -l
total 3748
-rw-r--r-- 1 ngs_user ngs_user 1408388 2011-11-14 09:55 maize_in.illumina.fasta
-rw-r--r-- 1 ngs_user ngs_user 1918848 2011-11-14 09:55 maize_in.illumina.fasta.qual
-rw-r--r-- 1 ngs_user ngs_user 506432 2011-11-14 09:55 maize_in.sanger.fasta
-rw-r--r-- 1 ngs_user ngs_user 0 2011-11-14 09:55 maize_in.sanger.fasta.qual
----------------------------------------------------------------------------------
and the 20111115_0204 dir like this:
gs_user@ngsmachine:~/ngs_workshop/maize/assembly/20111115_0204$ ls -l
total 4
lrwxrwxrwx 1 ngs_user ngs_user 32 2011-11-15 03:04 maize_in.illumina.fasta -> ../input/maize_in.illumina.fasta
lrwxrwxrwx 1 ngs_user ngs_user 37 2011-11-15 03:04 maize_in.illumina.fasta.qual -> ../input/maize_in.illumina.fasta.qual
lrwxrwxrwx 1 ngs_user ngs_user 30 2011-11-15 03:04 maize_in.sanger.fasta -> ../input/maize_in.sanger.fasta
lrwxrwxrwx 1 ngs_user ngs_user 35 2011-11-15 03:04 maize_in.sanger.fasta.qual -> ../input/maize_in.sanger.fasta.qual
drwxr-xr-x 2 ngs_user ngs_user 4096 2011-11-15 03:04 result
--------------------------------------------------------------------
and the result dir like this:
ngs_user@ngsmachine:~/ngs_workshop/maize/assembly/20111115_0204/result$ ls -l
total 0
----------------------------------------------------------------------
I found there is no mira soft in the
/usr/local/lib/python2.6/dist-packages/ext/bin/linux/64bit dir

Or you can tell me how to use the ngs_backbone assembly the EST reads
wait your answers!

Best regards,
lyuan

[peio]

Hi lyuan,
Few releases ago we removed mira assembly analysis from ngs_backbone. It takes to long and requires a lot of memory and sometimes (In our case ) you have to run it in another more powerful machine.

If you need to assemble the reads you can download mira[1] and run it outside of ngs_backbone.
Ngs_backbone helps you preparing the input files(renaming and joining) to run mira.

Use prepare_mira_assembly for that.

Regars
Peio Ziarsolo

[1] http://sourceforge.net/projects/mira...s/MIRA/stable/

[tt.tom]

hi
thanks your answers!and I met another problem,after the mira_assembly,annotate_orfs,how to do the next annotate step ,if there any file to introduce the ngs_backbone annotate usage,thanks !
best wishs!
lyuan