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Bowtie 2 NEWS
=============
Bowtie 2 is now available for download from the project website,
http://bowtie-bio.sf.net/bowtie2. 2.0.0-beta1 is the first version released to
the public and 2.0.0-beta6 is the latest version. Bowtie 2 is licensed under
the GPLv3 license. See `COPYING' file for details.
Reporting Issues
================
Please report any issues using the Sourceforge bug tracker:
https://sourceforge.net/tracker/?group_id=236897&atid=1101606
Version Release History
=======================
Version 2.0.0-beta6 - May 7, 2012
* Bowtie 2 now handles longer reads in a more memory-economical fashion,
which should prevent many out-of-memory issues for longer reads.
* Error message now produced when -L is set greater than 32.
* Added a warning message to warn when bowtie2-align binary is being run
directly, rather than via the wrapper. Some functionality is provided by
the wrapper, so Bowtie 2 should always be run via the bowtie2 executable
rather than bowtie2-align.
* Fixed an occasional crashing bug that was usually caused by setting the
seed length relatively short.
* Fixed an issue whereby the FLAG, RNEXT and PNEXT fields were incorrect for
some paired-end alignments. Specifically, this affected paired-end
alignments where both mates aligned and one or both mates aligned
non-uniquely.
* Fixed issue whereby compressed input would sometimes be mishandled.
* Renamed --sam-* options to omit the "sam-" prefix for brevity. The old
option names will also work.
* Added --no-unal option to suppress SAM records corresponding to unaligned
reads, i.e., records where FLAG field has 0x4 set.
* Added --rg-id option and enhanced the documentation for both --rg-id and
--rg. Users were confused by the need to specify --rg "ID:(something)" in
order for the @RG line to be printed; hopefully this is clearer now.
* Index updates: indexes linked to in the right-hand sidebar have been
updated to include the unplaced contigs appearing in the UCSC "random"
FASTA files. This makes the indexes more complete. Also, an index for
the latest mouse assembly, mm10 (AKA "GRCm38") has been added.
Version 2.0.0-beta5 - December 14, 2011
* Added --un, --al, --un-conc, and --al-conc options that write unpaired
and/or paired-end reads to files depending on whether they align at least
once or fail to align.
* Added --reorder option. When enabled, the order of the SAM records output
by Bowtie 2 will match the order of the input reads even when -p is set
greater than 1. This is disabled by default; enabling it makes Bowtie 2
somewhat slower and use somewhat more memory when -p is set greater than
1.
* Changed the default --score-min in --local mode to G,20,8. This ought to
improve sensitivity and accuracy in many cases.
* Improved error reporting.
* Fixed some minor documentation issues.
* Note: I am aware of an issue whereby longer reads (>10,000 bp) drive the
memory footprint way up and often cause an out-of-memory exception. This
will be fixed in a future version.
Version 2.0.0-beta4 - December 5, 2011
* Accuracy improvements.
* Speed improvements in some situations.
* Fixed a handful of crashing bugs.
* Fixed some documentation bugs.
* Fixed bug whereby --version worked incorrectly.
* Fixed formatting bug with MD:Z optional field that would sometimes fail to
follow a mismatch with a number.
* Added -D option for controlling the maximum number of seed extensions that
can fail in a row before we move on. This option or something like it
will eventually replace the argument to -M.
* Added -R option to control maximum number of times re-seeding is attempted
for a read with repetitive seeds.
* Changed default to --no-dovetail. Specifying --dovetail turns it back on.
* Added second argument for --mp option so that user can set maximum and
minimum mismatch penalties at once. Also tweaked the formula for
calculating the quality-aware mismatch penalty.
Version 2.0.0-beta3 - November 1, 2011
* Accuracy improvements.
* Speed improvements in some situations.
* Fixed a handful of crashing bugs.
* Fixed a bug whereby number of repetitively aligned reads could be
misreported in the summary output.
Version 2.0.0-beta2 - October 16, 2011
* Added manual, both included in the download package and on the website.
The website will always have the manual for the latest version.
* Added Linux 32-bit and 64-bit binary packages. Mac OS X packages to come.
Still working on a Windows package.
* Fixed a bug that led to crashes when seed-alignment result memory was
exhausted.
* Changed the --end-to-end mode --score-min default to be less permissive.
The previous threshold seemed to be having an adverse effect on accuracy,
though the fix implemented in this version comes at the expense of some
sensitivity.
* Changed the --end-to-end mode -M default to be lower by 2 notches. This
offsets any detrimental effect that the previous change would have had on
speed, without a large adverse impact on accuracy. As always, setting -M
higher will yield still greater accuracy at the expense of speed.
Version 2.0.0-beta1 - September 22, 2011
* First public release.
* Caveats: as of now, the manual is incomplete, there's no tutorial, and no
example genome or example reads. All these will be fixed in upcoming
releases.
* Only a source package is currently available. Platform-specific binaries
will be included in future releases.
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