NxTrim v0.4.3

• fixed a bad bug where a partial-but-perfect adapter match exact at the end of a read could be missed
• improved logging and error checking

NxTrim v0.4.2

• bugfixes that improve detection of malformed mate pairs
• minor speed ups
• added --aggressive mode which gives more sensitive adapter detection

NxTrim v0.4.1

Various bugfixes and minor improvements

• added more stdout functionality #20 #18 #19
• bugfixes #17
• changed some confusing command line arguments

nxtrim v0.4.0

• removed boost dependencies
• minor bugfixes

v0.3.2-alpha

minor changes

v0.3.0-alpha

• various minor improvements/bugfixes that give a modest improvement to the trimmed libraries
• added --separate flag to optionally produce separate files for R1/R2 (rather than interleaved)
• clearer counting of virtual libraries int stdout

Corresponds to results published in

http://bioinformatics.oxfordjournals.org/content/early/2015/02/05/bioinformatics.btv057.abstract

v0.2.2-alpha

Minor fixes to Makefile/versioning.

v0.2.0-alpha

We have made a number of minor improvements to to the trimming logic and added some new functionality.

Initial release

This release corresponds to the bacterial assembly results in the following pre-print:

http://dx.doi.org/10.1101/007666

We have found good results with 2x150bp Nextera Mate-Pair data on bacterial assemblies using NxTrim. There is no reason to think it will not work well with, say 2x250bp libraries, but it is untested.

The accuracy/functionality of the this tool is likely to continue to improve as we evaluate new libraries and assemblers.