June 29th, 2009· Fix for paired-end crashing bug in Windows version. src and win32 packages updated. Mac and Linux version are unaffected.
May 15th, 2009· Fixed an issue where bowtie --best would sometimes use excessive
· amounts of memory to store path descriptors. There is now a per-
· thread 32-MB ceiling (configurable with new option --chunkmbs
· ) on the memory taken by path descriptors. If the ceiling is
· exceeded Bowtie will skip the offending read, print a warning
· message identifying the read, and continue.
· More options are available for defining the quality-value format,
· including new --phred64-quals/--solexa1.3-quals options
· appropriate for the 64-based-Phred output of Illumina's GA
April 13th, 2009· Paired-end alignment is now available in all alignment modes,including all -n modes.
· best now provides better guarantees. Reported alignments are now guaranteed to be "best" both in terms of stratum (i.e. number
· of mismatches, or mismatches in the seed in the case of -n mode),
· and in terms of the quality values at the mismatched position(s).
· Stratum always trumps quality when determining best alignments.
· Also, --best mode resolves the strand bias issue (see manual for a
· discussion of the issue).
· Speed improvements for --best mode in most alignment modes.
· Major speed improvement for the -v 3 alignment mode (except when-z is also used)
· The "Reported X alignments..." message is now printed to stderr rather than stdout. Only alignments are written to stdout.
· In bowtie-maqconvert, read names longer than Maq's limit (36) are now truncated to a suffix of the original name, rather than a prefix. This mimics Maq's behavior and prevents "/1" and "/2" suffixes for paired-end reads from being destroyed.
· Added --alfq/--alfa options to dump aligned reads to FASTQ and/or FASTA files.
· Removed many extraneous source files.
March 12th, 2009· Added paired-end alignment for -v 2 and -v 3 alignment modes (-n modes coming soon).
· Minor bug fixes and speed improvements for all paired-end modes.
· Added -s/--skip option to skip over the first reads or pairs in the input.
· --unfq/--unfa/--maxfq/--maxfa modes no longer create empty output files.
· All Bowtie tools now compile under GCC 4.3.3.
· Fixed bug whereby bowtie -b would sometimes write garbage into the reference offset field.
· Paired-end info is now persisted in the -b format, allowing bowtie-maptool output to add "/1" and "/2" suffixes as appropriate.
February 20th, 2009· Added some preliminary support for paired-end alignment in -v 0 and -v 1 modes. -1/-2 options to specify the paired-end files, -I/-X to specify min and max insert sizes, and --fr/--rf/--ff specify relative orientation of upstream and downstream mates. bowtie-build now builds two additional files: NAME.3.ebwt and NAME.4.ebwt. Together, these files store a bitpacked version of the reference and they are required for paired-end alignment. If your index does not include these files and you would like to perform a paired-end alignment, you will have to rebuild the index with bowtie-build version 0.9.9 or later. Paired-end alignment is not compatible with -z mode, and it incurs about a 30% greater memory overhead than single-end mode.
· Pre-built indexes available from Bowtie website have been updated to include .3/.4.ebwt index files. These new pre-built indexes are no longer compatible with bowtie versions prior to 0.9.8.
· New -B/--offbase option allows user to specify how bowtie numbers reference positions in its output. E.g. -B 1 causes bowtie to number leftmost char as 1. -B 0 is the default, but -B 1 will likely become the default in the 1.0 release.
· Fixed a bug that caused trimming options -3 and -5 not to work properly in -r (raw input) mode.
· bowtie-build now prints a friendly error message and exits if an input file doesn't exist.
· Fixed a bug that caused the Win32 version of bowtie to hang just before it would normally have exited.
· Fixed bug that could prevent successful read-in of very large (>1GB) .2.ebwt index files.
· Removed --maxns option since it's mostly redundant with what -v and -n already do.
· Removed --ntoa option.
· bowtie usage message is now divided into sections for clarity.
January 8th, 2009Fixed all known problems with the --unfa/--unfq options:
· They now work properly with multiple threads.
· Fixed issue where sequence and quals were sometimes reversed.
· Fixed other issues causing spurious omission of unaligned reads.
· Added --maxfa/--maxfq options so that reads that don't align due to the -m limit can be dumped separately from reads that don't align at all.
· Alignment output is now guaranteed to be "deterministic" even when multiple threads are used. I.e., given the same input reads (in any order) and the same --seed, bowtie will produce the same alignments every time it is run, though not necessarily in the same order. This does not hold across different versions of bowtie.
· Multiple other bug fixes.
November 26th, 2008· --unfa/--unfq options cause bowtie to dump unaligned reads to FASTA and/or FASTQ files.
· bowtie-build now selects its memory-efficiency parameters (--bmax, --dcv, --packed) automatically by default; this makes it far easier to build an index under memory constraints by eliminating tedious trail-and-error. New -a option disables this, yielding old behavior.
· bowtie-build-packed is no longer a separate binary. Supplying the new -p/--packed argument to bowtie-build is the new equivalent.
· New tool bowtie-maptool converts between Bowtie's output formats.
· New tool bowtie-inspect recreates reference strings from Bowtie index.
· Renamed bowtie-convert to bowtie-maqconvert for clarity.
· New universal Mac binary combines i386 & x86_64 binaries. PowerPC still not supported.
· Added --nomaqround option to bowtie.
· Fixed memory leaks in bowtie.
· Switched to a new scheme for mapping positions in "joined" reference string to positions in original strings. This changes the index format. bowtie-build's --oldpmap parameter reverts to the old format. Versions of bowtie prior to 0.9.8 cannot search indexes produced by bowtie-build 0.9.8 unless bowtie-build is run with --oldpmap. bowtie 0.9.8 can search either index format. Pre-built indexes are still in the old format, but will switch to new format when Bowtie 1.0 is released.
November 12th, 2008· Fixed an issue that caused a spurious loss of sensitivity between Bowtie versions 0.9.6 and 0.9.7 in certain modes.
November 10th, 2008· Added new reporting option -m which suppresses all alignments for a particular read if more than reportable alignments exist for it.
· Threads now buffer all alignments for a particular read/phase then output all alignments in one critical section. This guarantees that all alignments for a given read/phase appear in one consecutive block of the output, even when multiple threads are operating in parallel.
· Separated the quality-conversion and parsing aspects of the old --solexa-quals argument into separate arguments: --solexa-quals (quality conversion) and --integer-quals (parsing).
· bowtie-convert now handles the new (post-0.7.0) Maq alignment format. The new format allows Maq tools to handle reads up to 127 bases, whereas the old format was limited to 63 bases. Added a -o option to opt for the old Maq format.
· New --refout argument sends alignments to a set of files named refXXXXX.map, where XXXXX is the 0-padded index of the reference sequence aligned to. Useful for dealing with large datasets aligned to, e.g., the assembled human genome.
· Improved tutorial to use a simple simulated read set (included) to do SNP calls with Maq.
· Added --nota option to bowtie-build
· Fixed make_h_sapiens_asm.sh script to include mitochondrial DNA.
October 27th, 2008· 'bowtie' now supports a host of options that allow the user to specify which and how many valid alignments to report per read. The default is still to report 1 "good" alignment, which is by far the fastest mode. See -k/-a/--best/--nostrata options described in the manual for details.
· 'bowtie' now supports reads up to 1024 bases long. Note that for reads much longer than, say, 35 bases, the user must be careful to set alignment policy parameters (especially -e) appropriately.
· --fast flag eliminated, double-index mode is now the default. Added the -z/--phased flag to revert to phased, half-index mode.
· --concise output mode now officially supported. Now outputs one alignment per line.
· Changed 'bowtie-build' default back to --bmaxdivn 4.
· -h/--help now prints much more verbose help for 'bowtie' and 'bowtie-build' (verbatim from MANUAL file)
· BWT-searching code streamlined; much old code eliminated
September 10th, 2008· Major reference-name bug fixes to bowtie-convert
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