MiModD / Blog: Recent posts

As the result of about a year of work it is quite a leap forward.

It is still lacking support for Android, autonomous driving and you can't run it inside any VR, but we've added:

• two new tools:
  rebase for migrating nucleotide positions from one genome release to another
  index to create indices for various file formats supported by MiModD

• a new mapping mode, Variant Allele Contrast Mapping... read more

This version fixes a number of annoying bugs reported for the last version and makes MiModD more platform-independent and user-friendly.

With the new version we are also introducing the third member of our family of prebuilt Galaxy bundles. Besides OS X and Ubuntu users, Fedora users can now try a fully featured MiModD running inside a preconfigured local Galaxy server with no installation effort at all!

You may not be aware of it, but when you installed MiModD, it came with fully functional builds of samtools and bcftools. Their read-for-use executables are in the package bin folder, which you can find by running:

python3 -m MiModD.config

, taking note of the path reported on the first line of output and appending /bin to it.
Feel free to use them for whatever task MiModD does not let you do directly!... read more

Nacreous clouds are extraordinary, stratospheric clouds.
NacreousMap (not just regular CloudMap) is the name of the new mapping-by-sequencing engine added to MiModD in version 0.1.7. Its code is the result of merging our previous linkage analysis code with a complete rewrite of the CloudMap Hawaiian Variant and EMS Variant Density Mapping tools.
The upcoming version 0.1.7.1 (due next week) features several bug-fixes and small enhancements of NacreousMap, which together with the previously available features make NacreousMap truly superior to CloudMap.... read more

The CloudMap Galaxy workflows rely on GATK tools such as the Unified Genotyper.
Over the past year, there have been numerous reports by users that this tool fails with out of memory errors on the main Galaxy server preventing users from running their workflows (see for example https://biostar.usegalaxy.org/p/10504/).

Remember: MiModD can fully replace the CloudMap workflows!

You will only need the CloudMap: Hawaiian Variant Mapping with WGS data tool on the main Galaxy server for visualizing the results.

some highlights:

• the cloudmap tool has been improved substantially allowing now for three-sample mapping analyses and using a more robust algorithm for the detection of informative variants

• filtering out anomalous overlapping read pairs from paired-end alignments has been improved: in the snap tool, the old --max-mate-overlap option has been dropped in favour of a new --discard-overlapping-mates option, which allows more fine-grained control over which types of overlapping mates should be removed... read more

We have updated our bundles of MiModD with a preconfigured Galaxy instance to the new release 0.1.5.

If you have OS X (10.8+) or Ubuntu 14.04, you can try MiModD and its Galaxy interface without any installation. Just download the bundle archive, unpack it and start up Galaxy.

The bundles along with usage instructions can be found here.

Starting with the new release 0.1.5 MiModD can be installed directly into Galaxy from the central Galaxy Tool Shed. To install the whole package with all Galaxy tool wrappers install suite_mimodd_0_1_5.

The new release 0.1.5 not only brings a major refactoring of some core tools in the package, which makes analyses with MiModD much more efficient.
It is also better tested than any previous release and includes dozens of bug-fixes.

We have finally managed to put together the bundled distribution for Mac OS 10.8 and above.
We have fixed several bugs found in the previous Mac OS bundle and are confident that the new release will work for most Macintosh users.
Let us know if you still run into problems.

Version 0.1.3 of MiModD is here and brings several bug-fixes and two useful new features (which we will have a closer look at in one of the next posts).

Note that we also upgraded our bundled distribution for Ubuntu to the new version.

Here, we took the opportunity to update also the embedded Galaxy server to its April 2014 release and to improve its preconfiguration substantially as explained in the readme.... read more