Minimap2-2.8 (r672)

Notable changes in this release include:

• Speed up short-read alignment by ~10%. The overall mapping accuracy stays
  the same, but the output alignments are not always identical to v2.7 due to
  unstable sorting employed during chaining. Long-read alignment is not
  affected by this change as the speedup is short-read specific.

• Mappy now supports paired-end short-read alignment (#87). Please see
  python/README.rst for details.

• Added option --for-only and --rev-only to perform alignment against the
  forward or the reverse strand of the reference genome only (#91).

• Alleviated the issue with undesired diagonal alignment in the self mapping
  mode (#10). Even if the output is not ideal, it should not interfere with
  other alignments. Fully resolving the issue is intricate and may require
  additional heuristic thresholds.

• Enhanced error checking against incorrect input (#92 and #96).

For long query sequences, minimap2 should output identical alignments to v2.7.

(2.8: 1 February 2018, r672)

Minimap2-2.7 (r654)

This release fixed a bug in the splice mode and added a few minor features:

• Fixed a bug that occasionally takes an intron as a long deletion in the
  splice mode. This was caused by wrong backtracking at the last CIGAR
  operator. The current fix eliminates the error, but it is not optimal in
  that it often produces a wrong junction when the last operator is an intron.
  A future version of minimap2 may improve upon this.

• Support high-end ARM CPUs that implement the NEON instruction set (#81).
  This enables minimap2 to work on Raspberry Pi 3 and Odroid XU4.

• Added a C API to construct a minimizer index from a set of C strings (#80).

• Check scoring specified on the command line (#79). Due to the 8-bit limit,
  excessively large score penalties fail minimap2.

For genomic sequences, minimap2 should give identical alignments to v2.6.

(2.7: 9 January 2018, r654)

Minimap2-2.6 (r623)

This release adds several features and fixes two minor bugs:

• Optionally build an index without sequences. This helps to reduce the
  peak memory for read overlapping and is automatically applied when
  base-level alignment is not requested.

• Approximately estimate per-base sequence divergence (i.e. 1-identity)
  without performing base-level alignment, using a MashMap-like method. The
  estimate is written to a new dv:f tag.

• Reduced the number of tiny terminal exons in RNA-seq alignment. The current
  setting is conservative. Increase --end-seed-pen to drop more such exons.

• Reduced the peak memory when aligning long query sequences.

• Fixed a bug that is caused by HPC minimizers longer than 256bp. This should
  have no effect in practice, but it is recommended to rebuild HPC indices if
  possible.

• Fixed a bug when identifying identical hits (#71). This should only affect
  artifactual reference consisting of near identical sequences.

For genomic sequences, minimap2 should give nearly identical alignments to
v2.5, except the new dv:f tag.

(2.6: 12 December 2017, r623)

Minimap2-2.5 (r572)

This release fixes several bugs and brings a couple of minor improvements:

• Fixed a severe bug that leads to incorrect mapping coordinates in rare
  corner cases. This bug was introduced by 13b66aa and affects v2.3 and v2.4.

• Fixed underestimated mapping quality for chimeric alignments when the whole
  query sequence contains many repetitive minimizers, and for chimeric
  alignments caused by Z-drop.

• Fixed two bugs in Python binding: incorrect strand field (#57) and incorrect
  sequence names for Python3 (#55).

• Improved mapping accuracy for highly overlapping paired ends.

• Added option -Y to use soft clipping for supplementary alignments (#56).

(2.5: 11 November 2017, r572)

Minimap2-2.4 (r555)

As is planned, this release focuses on fine tuning the base algorithm. Notable
changes include

• Changed the mapping quality scale to match the scale of BWA-MEM. This makes
  minimap2 and BWA-MEM achieve similar sensitivity-specificity balance on real
  short-read data.

• Improved the accuracy of splice alignment by modeling one additional base
  close to the GT-AG signal. This model is used by default with -x splice.
  For SIRV control data, however, it is recommended to add --splice-flank=no
  to disable this feature as the SIRV splice signals are slightly different.

• Tuned the parameters for Nanopore Direct RNA reads. The recommended command
  line is -axsplice -k14 -uf (#46).

• Fixed a segmentation fault when aligning PacBio reads (#47 and #48). This
  bug is very rare but it affects all versions of minimap2. It is also
  recommended to re-index reference genomes created with map-pb. For human,
  two minimizers in an old index are wrong.

• Changed option -L in sync with the final decision of hts-specs: a fake
  CIGAR takes the form of <readLen>S<refLen>N. Note that -L only enables
  future tools to recognize long CIGARs. It is not possible for older tools to
  work with such alignments in BAM (#43 and #51).

• Fixed a tiny issue whereby minimap2 may waste 8 bytes per candidate
  alignment.

The minimap2 technical note has also been updated to reflect recent changes.

(2.4: 6 November 2017, r555)

Minimap2-2.3 (r531)

This release comes 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,
plus the addition of spliced long-read alignment. The next couple of releases
will focus on fine tuning the base algorithm.

(2.3: 22 October 2017, r531)

Minimap2-2.2 (r409)

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)

Minimap2-2.1.1 (r341)

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)

Minimap2-2.1 (r311)

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.

(2.1: 25 August 2017, r311)

Minimap2-2.0 (r275)

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.

(2.0: 8 August 2017, r275)