How big is this news? Well, bigger than 4 GB, that's for sure.
A while back I brought up this issue on BioStars.
From the Bowtie2 news page:
Version 2.2.0 - February 10, 2014
- Improved index querying efficiency using "population count" instructions available since SSE4.2
- Added support for large and small indexes, removing 4-billion-nucleotide barrier. Bowtie 2 can now be used with reference genomes of any size.
- Fixed bug that could cause bowtie2-build to crash when reference length is close to 4 billion.
- Added a CL: string to the @PG SAM header to preserve information about the aligner binary and paramteres.
- Fixed bug that could cause bowtie2-build to crash when reference length is close to 4 billion.
- No longer releasing 32-bit binaries. Simplified manual and Makefile accordingly.
- Credits to the Intel® enabling team for performance optimizations included in this release. Thank you!
- Phased out CygWin support. MinGW can still be used for Windows building.
- Added the .bat generation for Windows.
- Fixed some issues with some uncommon chars in fasta files.
- Fixed wrappers so bowtie can now be used with symlinks.
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