Software packages for next gen sequence analysis

[alig]

Consed is very similar to gap4 and now assembles illumina short reads.

I have been happy with the assembly to a reference sequence & the contig viewer & searching for highly discrepant regions.

hope this is of help

alig

[xiechao]

CNV-seq

a package to detect DNA copy number variation using shotgun sequencing.
http://tiger.dbs.nus.edu.sg/cnv-seq/
http://www.biomedcentral.com/1471-2105/10/80

[WJW-Davy]

MapView: a short reads alignment viewer with genetic variation analysis, visualization of short reads alignment on desktop computer

http://evolution.sysu.edu.cn/mapview/

[Batalov]

I didn't see MACS and PeakSeq among the ChIP-seq peak callers. Those should be added.

Seconded. MACS is a useful tool.

[xuer]

thanks swbarnes2

i think i will post a query on the UCSC listserver
[email protected]
and see if someone like Jim Kent is thinking about some utility that could facilitate reference assembly on a local Genome Browser ... he's the guy i think who initiated BLAT and isPCR on their site

http://genome.ucsc.edu/

the browser can be installed locally and used with any genome ... but without taking into account quality values from the reads its hard to imagine not getting just a mess doing a BLAT-like alignment ... i think

RudyS

Is there anybody have the experience to install UCSC locally with other genome database like arabidopsis? I hope I can find a detailed procedure to set it locally.
Thanks!

[RudyS]

xuer
the browser is well documented ... suggest you write to the nice folks on the listserver there

[email protected]

Rudy

[Joann]

Meeting in Berlin this month

Xuer, you might also access TAIR scientists who will be attending the International Biocuration Conference in Berlin later this month.
http://projects.eml.org/sdbv/events/.../schedule.html

[xuer]

RudyS,Thank you for the reply.for me the Installation if UCSC is finished, next i need to set the arabidopsis assembly. hopefully it goes well.

Joann, Thank you for the information.The topics are interesting , i hope i could be there.

[Genomatix]

How about Genomatix?

Hate to be so blatantly commercial, but in the "not for free" category, you should add Genomatix. No sales pitch here...but check out the vendor forum! Complete analysis capabilities for all current platforms...thanks.

[sparks]

Release V2.03.12 of Novoalign is out. This release improves performance especially for longer reads and is a 4-5 times faster on 45bp reads against Human. Longer reads have improved even more. Performance improvement is more pronounced when allowing more mismatches (higher thresholds).

It also seems our web site has been blocked in China so if any one in China wants a copy of novoalign please email me at colin at novocraft dot com. I'll create a mailing list and keep you informed of any updates etc.

[bioinfosm]

I think it will be a good idea to include RNA-SEQ tools in the huge table. The one tool I know for that = erange

[ewilbanks]

Any more ChIP-seq analysis tools that we should add here?

Also, does anyone know if the program from the Poisson mixture method paper is publicly available?:
http://www.biomedcentral.com/1471-2164/9/S2/S23

Or if anything has been published about the ChIP-seq Analysis server?
http://ccg.vital-it.ch/chipseq/

[dan]

Any more ChIP-seq analysis tools that we should add here?

The Bioconductor 'chipseq' package / programs should be added for sure! See also the other thread on this topic:

http://seqanswers.com/forums/showthread.php?t=742

[mbjohnson]

RNA-seq tools?

I think it will be a good idea to include RNA-SEQ tools in the huge table. The one tool I know for that = erange

I'd like to second the call for including RNA-seq tools, e.g. ERANGE, TOPHAT, G-Mo.R-se... any others??

[jhui]

I'd like to second the call for including RNA-seq tools, e.g. ERANGE, TOPHAT, G-Mo.R-se... any others??

Also RSAT