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Name: bowtie2 | Distribution: openSUSE Leap 15.2 |
Version: 2.3.5.1 | Vendor: openSUSE |
Release: lp152.2.2 | Build date: Sat May 16 17:59:00 2020 |
Group: Productivity/Scientific/Other | Build host: goat13 |
Size: 3698929 | Source RPM: bowtie2-2.3.5.1-lp152.2.2.src.rpm |
Packager: https://bugs.opensuse.org | |
Url: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | |
Summary: Fast and memory-efficient short read aligner |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
GPL-3.0-only
* Tue May 12 2020 Guillaume GARDET <guillaume.gardet@opensuse.org> - Fix aarch64 build with: * simde sources * export POPCNT_CAPABILITY=0 * Sat Nov 30 2019 Atri Bhattacharya <badshah400@gmail.com> - Use %%license to install LICENSE file. * Thu Nov 07 2019 Atri Bhattacharya <badshah400@gmail.com> - Update to version 2.3.5.1: * Added official support for BAM input files. * Added official support for CMake build system. * Added changes to Makefile for creating Reproducible builds [gh#BenLangmead/bowtie2#210]. * Fix an issue whereby building on aarch64 would require patching sed commands [gh#BenLangmead/bowtie2#243]. * Fix an issue whereby `bowtie2` would incorrectly throw an error while processing `--interleaved` input. - Changes from version 2.3.5: * Added support for obtaining input reads directly from the Sequence Read Archive, via NCBI's [NGS language bindings](https://github.com/ncbi/ngs). This is activated via the [`--sra-acc`](manual.shtml#bowtie2-options-sra-acc) option. This implementation is based on Daehwan Kim's in [HISAT2](https://ccb.jhu.edu/software/hisat2). Supports both unpaired and paired-end inputs. * Bowtie 2 now compiles on ARM architectures (via [gh#BenLangmead/bowtie2#216]. * `--interleaved` can now be combined with FASTA inputs (worked only with FASTQ before). * Fixed issue whereby large indexes were not successfully found in the `$BOWTIE2_INDEXES` directory. * Fixed input from FIFOs (e.g. via process substitution) to distinguish gzip-compressed versus uncompressed input. * Fixed issue whereby arguments containing `bz2` `lz4` were misinterpretted as files. * Fixed several compiler warnings. * Fixed issue whereby both ends of a paired-end read could have negative TLEN if they exactly coincided * Fixed issue whereby `bowtie2-build` would hang on end-of-file [gh#BenLangmead/bowtie2#228]. * Fixed issue whereby wrapper script would sometimes create zombie processes [gh#BenLangmead/bowtie2#51]. * Fixed issue whereby `bowtie2-build` and `bowtie2-inspect` wrappers would fail on some versions of Python/PyPy. * Replaced old, unhelpful `README.md` in the project with a version that includes badges, links and some highlights from the manual. * Wed Feb 28 2018 badshah400@gmail.com - Update to version 2.3.4.1: * Fixed an issue with --reorder that caused bowtie2 to crash while reordering SAM output - Changes from version 2.3.4: * Fixed major issue causing corrupt SAM output when using many threads (-p/--threads) on certain systems. * Fixed an issue whereby bowtie2 processes could overwrite each others' named pipes on HPC systems. * Fixed an issue causing bowtie2-build and bowtie2-inspect to return prematurely on Windows. * Fixed issues raised by compiler "sanitizers" that could potentially have caused memory corruption or undefined behavior. * Added the "continuous FASTA" input format (-F) for aligning all the k-mers in the sequences of a FASTA file. Useful for determining mapability of regions of the genome, and similar tasks. - Run sed on binaries to modify env based hashbangs to ones that directly call executables. - Drop bowtie2-gcc6.patch; incorporated upstream. * Mon Sep 04 2017 mpluskal@suse.com - Update to version 2.3.2: * Added support for interleaved paired-end FASTQ inputs (--interleaved) * Now reports MREVERSE SAM flag for unaligned end when only one end of a pair aligns * Fixed issue where first character of some read names was omitted from SAM output when using tabbed input formats. * Added --sam-no-qname-trunc option. * Fixed compilation error caused by pointer comparison issue in aligner_result.cpp * Removed termcap and readline dependencies introduced in v2.3.1 * Fixed compilation issues caused by gzbuffer function when compiling with zlib v1.2.3.5 and earlier. * Fixed issue that would cause Bowtie 2 hang when aligning FASTA inputs with more than one thread - Changes for version 2.3.0: * Code related to read parsing was completely rewritten to improve scalability to many threads. * TBB is now the default threading library. * Bowtie now uses a queue-based lock rather than a spin or heavyweight lock. * Unnecessary thread synchronization removed * Fixed issue with parsing FASTA records with greater-than symbol in the name * Changed default for --bmaxdivn to yield better memory footprint and running time when building an index with many threads - Add bowtie2-gcc6.patch (fixes compilation with gcc6+) - Build using optflags - Update download url - Small package cleanup with spec-cleaner * Thu May 05 2016 flyos@mailoo.org - Initial release
/usr/bin/bowtie2 /usr/bin/bowtie2-align-l /usr/bin/bowtie2-align-s /usr/bin/bowtie2-build /usr/bin/bowtie2-build-l /usr/bin/bowtie2-build-s /usr/bin/bowtie2-inspect /usr/bin/bowtie2-inspect-l /usr/bin/bowtie2-inspect-s /usr/share/doc/packages/bowtie2 /usr/share/doc/packages/bowtie2/AUTHORS /usr/share/doc/packages/bowtie2/MANUAL /usr/share/doc/packages/bowtie2/NEWS /usr/share/doc/packages/bowtie2/TUTORIAL /usr/share/doc/packages/bowtie2/VERSION /usr/share/licenses/bowtie2 /usr/share/licenses/bowtie2/LICENSE
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