[Bio-Linux] QIIME 1.9

[Tim Booth]

Dear All,

It's taken a while, but you can now upgrade to QIIME 1.9 on Bio-Linux 8.
The update should come through in the regular system updater.  If you
had update errors earlier today please try again as I fixed a couple of
things.

If you are still using Bio-Linux 7 and want this new software please
upgrade to Bio-Linux 8.

Important Notes:

1) Consistency of results with new tools

On Bio-Linux, QIIME uses the latest versions of component packages like
RDP-classifier, BWA, CD-HIT, etc. etc.  Also, QIIME will use the free program
vSearch in place of uSearch61.  This means that your results will not be identical
to the results obtained with the official QIIME installation.  You can run:

qiime print_qiime_config_all

to see exactly what you have installed.  If you need consistent results
with older or official versions of QIIME you should set up the software
as per the official instructions on the QIIME website.  If you want to
override just one particular tool, ensure that your path is set so that
the custom version takes precedence.  The standard way to do this
is to just install the alternative under /usr/local/bin.

2) Choice of database for taxonomy identification

When assigning taxonomy to sequences, the default method is uclust for
which you need to specify --id_to_taxonomy_fp and --reference_seqs_fp,
either on the command line or in your .qiime_config.  QIIME now ships
with a release of Greengenes you can use for this,
under /usr/share/qiime/data/gg_13_8_otus.  

If you want a quick classification, specify "rdp" as the assignment
method and the default RDP 16S database will be used.  You can also
specify --id_to_taxonomy_fp and --reference_seqs_fp to be used with the
rdp classifier, but be aware that retraining it on the Greengenes index
uses a fair chunk of RAM.

Finally...

The main delay in releasing the package for Bio-Linux was, as I
previously commented on the mailing list, that I've been busy ensuring
that QIIME can handle all the new tool versions.  Thanks for your
patience while I got this done.  I've tested as much as I can but if you
find bugs please let me know by posting on the
bio-linux at nebclists.nerc.ac.uk address and I'll try to fix them ASAP.
There may well be bugs - this is a very complex beast!

Best,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297