Archive for October, 2012

MG-RAST 3.2.4 release notes [October 2012]

Tuesday, October 23rd, 2012

Analysis page:
Barchart, tree, heatmap and PCoA visualizations have been added for the Lowest Common Ancestor analyses.

Upload page:
The upload page was modified to simplify the layout, grouping common functions together. The error handling was changed to make the messages displayed human readable and indicate the actions necessary to remedy the problems found.

Merging mate-pairs:

[Changed, see this FAQ entry for the current procedure]

The new ‘merge mate-pairs’ function on the Upload page allows users to upload and merge two separate fastq files which represent ordered paired end reads from the same sequencing run. The fastq-join utility (http://code.google.com/p/ea-utils/wiki/FastqJoin) is used to merge mate-pairs with a minimum overlap setting of 8bp and a maximum difference of 10% (parameters: -m 8 -p 10). Then, mate-pairs that have not been merged are joined by appending 10 N’s to the first read and then appending the reverse complemented paired read. These results are then merged into a single output file which can be submitted for analysis to MG-RAST.

Preprocessing:
In the preprocessing pipeline options, Sus Scrofa, NCBI v10.2 has been added to the list of species available for screening using bowtie.

Overview page:
The kmer profile and nucleotide position histogram is now displayed for amplicon datasets.

Bug fixes:
Miscellaneous bug fixes.