A beta version of Strand's Avadis NGS 1.3 is now available.
The beta release includes an experiment-specific analysis pipeline for small RNA data; COBWeb, a sequence data alignment algorithm based on the Burrows-Wheeler transform that is designed for gapped alignment of DNA and small RNA reads in FASTA and FASTQ files; and three new RNA-seq quantification and normalization options, among other capabilities.
Cufflinks 1.3.0 is available here.
The release includes improvements to the accuracy of Cuffdiff's isoform switching tests and fixes several bugs.
SoftGenetics has added an assembler for Life Technologies' Ion Torrent PGM sequencer to version 2.2 of its NextGENe software.
The "flow-based" assembler, dubbed Floton, treats homopolymer errors as substitution errors and corrects them during the assembly process. It also condenses sequences into flow calls of individual bases and condenses the number of bases in each flow so that insertions and deletions are converted into substitution errors, which improves the assembly.