minimap2/NEWS.md

Release 2.3-r531 (22 October 2017)
----------------------------------

This release come with many improvements and bug fixes:

 * The **sr** preset now supports paired-end short-read alignment. Minimap2 is
   3-4 times as fast as BWA-MEM, but is slightly less accurate on simulated
   reads.

 * Meticulous improvements to assembly-to-assembly alignment (special thanks to
   Alexey Gurevich from the QUAST team): a) apply a small penalty to matches
   between ambiguous bases; b) reduce missing alignments due to spurious
   overlaps; c) introduce the short form of the `cs` tag, an improvement to the
   SAM MD tag.

 * Make sure gaps are always left-aligned.

 * Recognize `U` bases from Oxford Nanopore Direct RNA-seq (#33).

 * Fixed slightly wrong chaining score. Fixed slightly inaccurate coordinates
   for split alignment.

 * Fixed multiple reported bugs: 1) wrong reference name for inversion
   alignment (#30); 2) redundant SQ lines when multiple query files are
   specified (#39); 3) non-functioning option `-K` (#36).

This release has implemented all the major features I planned five months ago,
with the addition of spliced long-read alignment. The next couple of releases
will focus on fine tuning of base algorithms.

(2.3: 22 October 2017, r531)



Release 2.2-r409 (17 September 2017)
------------------------------------

This is a feature release. It improves single-end short-read alignment and
comes with Python bindings. Detailed changes include:

 * Added the **sr** preset for single-end short-read alignment. In this mode,
   minimap2 runs faster than BWA-MEM, but is slightly less accurate on
   simulated data sets. Paired-end alignment is not supported as of now.

 * Improved mapping quality estimate with more accurate identification of
   repetitive hits. This mainly helps short-read alignment.

 * Implemented **mappy**, a Python binding for minimap2, which is available
   from PyPI and can be installed with `pip install --user mappy`. Python users
   can perform read alignment without the minimap2 executable.

 * Restructured the indexing APIs and documented key minimap2 APIs in the
   header file minimap.h. Updated example.c with the new APIs. Old APIs still
   work but may become deprecated in future.

This release may output alignments different from the previous version, though
the overall alignment statistics, such as the number of aligned bases and long
gaps, remain close.

(2.2: 17 September 2017, r409)



Release 2.1.1-r341 (6 September 2017)
-------------------------------------

This is a maintenance release that is expected to output identical alignment to
v2.1. Detailed changes include:

 * Support CPU dispatch. By default, minimap2 is compiled with both SSE2 and
   SSE4 based implementation of alignment and automatically chooses the right
   one at runtime. This avoids unexpected errors on older CPUs (#21).

 * Improved Windows support as is requested by Oxford Nanopore (#19). Minimap2
   now avoids variable-length stacked arrays, eliminates alloca(), ships with
   getopt_long() and provides timing functions implemented with Windows APIs.

 * Fixed a potential segmentation fault when specifying -k/-w/-H with
   multi-part index (#23).

 * Fixed two memory leaks in example.c

(2.1.1: 6 September 2017, r341)



Release 2.1-r311 (25 August 2017)
---------------------------------

This release adds spliced alignment for long noisy RNA-seq reads. On a SMRT
Iso-Seq and a Oxford Nanopore data sets, minimap2 appears to outperform
traditional mRNA aligners. For DNA alignment, this release gives almost
identical output to v2.0. Other changes include:

 * Added option `-R` to set the read group header line in SAM.

 * Optionally output the `cs:Z` tag in PAF to encode both the query and the
   reference sequences in the alignment.

 * Fixed an issue where DP alignment uses excessive memory.

The minimap2 technical report has been updated with more details and the
evaluation of spliced alignment:

 * Li, H. (2017). Minimap2: fast pairwise alignment for long nucleotide
   sequences. [arXiv:1708.01492v2](https://arxiv.org/abs/1708.01492v2).

(2.1: 25 August 2017, r311)



Release 2.0-r275 (8 August 2017)
--------------------------------

This release is identical to version 2.0rc1, except the version number. It is
described and evaluated in the following technical report:

 * Li, H. (2017). Minimap2: fast pairwise alignment for long DNA sequences.
   [arXiv:1708.01492v1](https://arxiv.org/abs/1708.01492v1).

(2.0: 8 August 2017, r275)



Release 2.0rc1-r232 (30 July 2017)
----------------------------------

This release improves the accuracy of long-read alignment and added several
minor features.

 * Improved mapping quality estimate for short alignments containing few seed
   hits.

 * Fixed a minor bug that affects the chaining accuracy towards the ends of a
   chain. Changed the gap cost for chaining to reduce false seeding.

 * Skip potentially wrong seeding and apply dynamic programming more frequently.
   This slightly increases run time, but greatly reduces false long gaps.

 * Perform local alignment at Z-drop break point to recover potential inversion
   alignment. Output the SA tag in the SAM format. Added scripts to evaluate
   mapping accuracy for reads simulated with pbsim.

This release completes features intended for v2.0. No major features will be
added to the master branch before the final v2.0.

(2.0rc1: 30 July 2017, r232)



Release r191 (19 July 2017)
---------------------------

This is the first public release of minimap2, an aligner for long reads and
assemblies. This release has a few issues and is generally not recommended for
production uses.

(19 July 2017, r191)