Researchers from the University of California, Berkeley, and the University of Maryland have released version 1.2.0 of the transcript assembly software Cufflinks here. The new release fixes several bugs and includes accuracy and performance improvements.
The National Center for Biotechnology Information has released its Variation Reporter Tool to match variant calls with variants in dbSNP or dbVar. The new tool is available here, and will provide detailed information on known alleles for the variant call. If the variant is not present in either database it will calculate whether it has a predicted functional consequence.
The NCBI has also added human variant call format files and human genotype XML files by gene to dbSNP, available here via FTP.
Researchers from Johns Hopkins School of Public Health have released Bowtie version 2.0 for aligning sequence reads to the reference. The new release, available here, includes accuracy improvements, speed improvements, and fixes several bugs.