BWA-MEM is the successor of BWA and BWA-SW. It has the following features:
Support of query sequences ranged from ~70bp to a few megabases. Except BWA-SW and Last, most read mappers would not work with >5kb query.
Fast. Similar to bowtie2 and twice as fast as BWA/BWA-SW/Cushaw2 for 100bp reads. Twice as fast as BWA-SW and several times faster than Bowtie2 and Cushaw2 for >500bp reads (even faster for 1kb reads).
Accurate. For 100bp simulated data, similar to Cushaw2 on accuracy and more accurate then Bowtie2 and BWA. Novoalign is still the most accurate.
Working with genomes with total length longer than 4GB. Except BWA since 0.6.x, other free BWT-based mappers have the 4GB limit.
More permissive (than BWA and GEM) to long gaps up to tens of bp for 100bp reads, or up to several hundred bp (tunable) for contig alignment.
Reporting chimeric alignment where different parts of the query mapped to different places. Note that multiple hits are overlapping alignments, but chimeric alignments are ideally non-overlapping. An aligner reporting multiple hits may not work well with chimeric alignments, in some cases.
Simpler command line interface and better multi-threading support (than BWA).
Automatically switching between the end-to-end and local alignment modes. End-to-end alignment reduces false negatives for variants towards the end of a read, but may add false positives for long indels towards the end; local alignment is the contrary. BWA-MEM attempts to choose the right mode for each read, instead of using one mode for all reads.
Better paired-end mapping (than BWA, BWA-SW and bowtie2). BWA-MEM uses a similar strategy to stampy and novoalign which jointly considers single-end alignment scores, insert size distribution and the possibility of chimeric pairs.
Exposing basic APIs for single-end alignment. (Bindings in other languages are welcomed.)
BWA-MEM however lacks the following features:
Working with very short reads. The performance and the accuracy of BWA-MEM will degrade.
Guaranteed sensitivity to hits within a certain edit distance threshold (as with BWA and GEM).
BWA-MEM is a component of BWA. The repository is hosted by github. The released packages are provided via SourceForge. The preprint of the manuscript and a poster (PDF) are also publicly available.
Have you tested BWA-MEM on PacBio reads? They are pretty long for sequencing reads, but have an error-rate between 11-17%...
How do I tune BWA to allow longer gaps for contig alignment? The default gap extension penalty is a int and set by default to 1. I don't see which other parameter to adjust for allowing longer gaps.