SeqAn - The C++ Library for Sequence Analysis - Release 1.4

[holtgrewe]

Hi everyone,

The SeqAn team is happy to announce the 1.4 Release of the SeqAn apps and libraries. This update includes all improvements and changes over the last two years since the 1.3 release. You can download the release packages at http://packages.seqan.de.

Some highlights are:

• New read mapping programs Masai (backtracks two string tries in parallel) and RazerS 3 (uses q-gram index filters and OpenMP).
• An efficient implementation of an FM index that combines good performance with low memory usage and can be iterated as a prefix trie via the string tree iterator interface.
• A new command line parser that facilitates the integration of programs into workflow engines such as KNIME or Galaxy.
• An extended and more robust I/O system, namely in the modules seq_io, gff_io, bam_io.

You can find a list of many more updates in our Trac wiki in the Changelog.
If you are upgrading from a previous release, you can learn about the new library content in the updated tutorial.
In case of questions or support, please send an email to our mailing list.

Have fun!
The SeqAn Team

[CrushChee]

Re:

I'm a new guy to bioinformatics.
i used tophat and cufflinks for my RNA-seq data to generate diff_out file.Until this step everything is fine.
then i started cummeRbund with my diff_out file, but always failed.

here is my command:
$ R
> library(cummeRbund)
> cuff_data <- readCufflinks('diff_out')
here is the problem:

Creating database diff_out/cuffData.db
Reading diff_out/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (unable to bind data for parameter ':status')

Highly appreciate your help.




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