The new version of Metaxa – Metaxa2 – which I first started talking about more than 1.5 years ago, has finally been determined to be so stable that we can officially release it! The release come around the same time as we submitted a paper describing the changes in it, but I will briefly go through the changes here:
Metaxa2 now handles extraction and classification of LSU rRNA sequences in addition to SSU rRNA
The classification engine has been completely redesigned, and now enables accuratetaxonomic classifications down to the genus – or in some cases – species level
The classification database has been updated, and is now based on the SILVA 111 release
The Metaxa2 Taxonomic Traversal Tool – metaxa2_ttt – has been added to the package, to ease the counting of rRNA sequences in different organism groups (at various taxonomic levels)
Metaxa2 adds support for paired-end libraries
It is now possible to directly input of sequences in FASTQ-format to Metaxa2
The support for libraries with short read lengths (~100 bp) has been vastly improved (and is now assumed to be the case for default settings)
Metaxa2 can do quality pre-filtering of reads in FASTQ-format
Metaxa2 adds support for the modern BLAST+ package (although the old blastall version is still default)
Compatibility with the HMMER 3.1 beta
Metaxa2 brings together a large set of features that we have been gradually incorporating since 2011, many of which have been dependent on each other. Most of the new features and changes are thoroughly explained in the manual. While we hope Metaxa2 is bug free, there will likely be bugs caused by usage scenarios we have not envisioned. I therefore encourage anyone who come across some unexpected behavior to send me an e-mail. Especially, I would like to know about how the software performs using HMMER 3.1 and BLAST+, where testing has been limited compared to older parts of the code.
We hope that you will find Metaxa2 useful, and that it will bring taxonomic assessment of metagenomes another step forward! Metaxa2 can be downloaded here.