Pacific Biosciences has launched new assembly and base-calling tools, HGAp and Quiver, available for download on its DevNet site.
HGAp performs de novo assembly using data from the PacBio long insert library and achieves greater than 99.999 percent (Q50) finished accuracy. The tool requires just one long-insert library prep and uses single-pass reads for the assembly rather than circular consensus sequencing reads, which reduces the number of SMRT cells required by around 50 percent, according to the company.
Quiver is an algorithm for calling consensus from multiple PacBio subreads using a hidden Markov model and both the base calls and QV metrics to infer the sequence.
Johns Hopkins Bloomberg School of Public Health has released Bowtie version 2.0.4, available here, which fixed a command-line parsing issue and an issue on Windows, and includes updated scripts and documentation.