Below is a very short list of software that was presented at GI2015. This is only a tiny slice of the tools and methods that were presented at the meeting, and the list is highly biased toward tools that I personally find interesting or useful to my own work (please don’t be offended if I omitted your stuff, and feel free to mention it in the comments).
Sleuth: R package for analyzing & reporting differential expression analysis from transcript abundances estimated with Kallisto.
Preprint: coming soon?
See also: The bear’s lair (http://lair.berkeley.edu/): reanalysis of published RNA-seq studies using kallisto+sleuth.
Rail: software for aligning many-sample RNA-seq data, producing alignments, genome coverage bigWigs, and splice junction BED files.
Genotype Query Tools (GQT): fast/efficient individual-level queries of large-scale variation data.
Centrifuge: a metagenomics classifier.
Mash: MinHash-based method for rapidly estimating pairwise distances between genomes or metagenomes.
VCFanno: ultrafast large-sample VCF annotation
Ginkgo: Interactive analysis and assessment of single-cell copy-number variations
StringTie: RNA-seq transcript assembly+quantification, with or without a reference. See paper for comparison to existing tools.