diff --git a/NEWS b/NEWS index d68c693..be7c035 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,47 @@ +Beta Release 0.7.0 (28 Feburary, 2013) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +This release comes with a new alignment algorithm, BWA-MEM, for 70bp-1Mbp query +sequences. BWA-MEM essentially seeds alignments with a variant of the fastmap +algorithm and extends seeds with banded affine-gap-penalty dynamic programming +(i.e. the Smith-Waterman-Gotoh algorithm). For typical Illumina 100bp reads or +longer low-divergence query sequences, BWA-MEM is about twice as fast as BWA +and BWA-SW and is more accurate. It also supports split alignments like BWA-SW +and may optionally output multiple hits like BWA. BWA-MEM does not guarantee +to find hits within a certain edit distance, but BWA is not efficient for such +task given longer reads, either, and the edit-distance criterion is arguably +not as important in long-read alignment. + +In addition to the algorithmic improvements, BWA-SW also implements a few +handy features, some of which are experimental: + + 1. BWA-MEM automatically infers pair orientation from a batch of single-end + alignments. It allows more than one orientations if there are sufficient + reads supporting them. This feature has not been tested on reads from + Illumina jumping library yet. + + 2. BWA-MEM optionally takes one interleaved fastq for paired-end mapping. It + is possible to convert a name-sorted BAM to an interleaved fastq on the fly + and feed the data stream to BWA-MEM for mapping. + + 3. BWA-MEM optionally copies FASTA/Q comments to the final SAM output. This + helps to transfer individual read annotations to the output. + + 4. BWA-MEM supports more advanced piping. Users can now run: + (bwa mem ref.fa '