Each day, we will present a short summary of interesting papers. Some of these will be considered in further detail later, when time permits. Please feel free to suggest any good paper you come across.
Trinity - Full-length transcriptome assembly from RNA-Seq data without a reference genome This is an excellent Category D algorithm that we have been using for the last few months for our RNAseq with very satisfactory result. The manuscript just came out in the paper version of Nature Biotech, but electronic version was available from their website for a few months. Previously we had been struggling with Velvet+Oases, which consumed large amount of memory. The memory handling of Trinity is excellent.
Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads This paper came out online last year, but we are starting to use their method. Most category A algorithms (mapping on reference genome) sacrifice speed for accuracy. Bowtie and BWA cannot go beyond more than few mismatches. Stampy is designed to overcome that shortcoming.
Dindel: Accurate indel calls from short-read data This is another category A algorithm directed towards finding insertion-deletions from short read data. Earlier algorithms searched for exact matches and short SNPs.
Yesterday was one of the most beautiful days of summer here and we decided to make a trip to Sunrise, Mount Rainier to get a close view of the peak. We walked on snow on a nearby hill (Wonderland trail, I believe) and enjoyed full view of the mountain. Hope this picture will bring some needed chill for east- coasters.