assemblotron

assemblotron copied to clipboard

Add RNAspades

1

http://bioinf.spbau.ru/en/rnaspades

blahah

http://www.genomebiology.com/2015/16/1/30 https://sourceforge.net/projects/rnaseqassembly

blahah

fixes to loading config file and a few other little things

1

cboursnell

Users may want to repeat the optimisation multiple times and take the average, or use vote-counting to choose candidate assemblies.

blahah

- Shared `Logger` instance - log at the appropriate level instead of `puts`ing - allow user to set loglevel as a commandline argument

blahah

In this strategy we partition the reads, and rather than sampling the partitions we optimise the assembly of each partition separately. Large partitions could be sampled down or diginormed.

blahah

When run with a small number of reads most assemblers have some combination of settings that is impossible, or which will produce an empty output file or no file at...

blahah

We need user docs in the form of a website. Developer docs can be generated from the source using rdoc.

blahah

Implement the same as in transrate. Relevant code: - https://github.com/Blahah/transrate/blob/master/bin/transrate#L13-L28 - https://github.com/Blahah/transrate/blob/master/bin/transrate#L80-L81 - https://github.com/Blahah/transrate/blob/master/bin/transrate#L164-L167 - https://github.com/Blahah/transrate/blob/master/lib/transrate.rb#L15-L25

blahah

blahah