The programs gmap and gsnap, for aligning rna-seq and dna-seq datasets to genomes, have evolved along with advances in biological methodology to handle longer reads, larger volumes of data, and new types of biological assays the genomic representation has been improved to include linear genomes that can compare sequences using single-instruction multiple-data (simd) instructions, compressed. Gsnap aligner download. Nodejs interface to the gsnap spliced aligner for rna-seq - olgabot/bionode-gsnap.
gsnap aligner download
Aligners spend a proportion of their time indexing the reference sequence to speed up the overall alignment now you can create and keep those indexes (bwa) or databases (gsnap), making it faster when you want to experiment with different parameters to improve an alignment or splice placement. Gsnap. gsnap (genomic short-read nucleotide alignment program) is a tool to align single- and paired-end reads to a reference genome. the gsnap algorithm is based on the seed-and-extend method and works on reads down to 14 nucleotides of length, and computes snp-tolerant alignments of various combinations of major and minor alleles. the algorithm can discover long-distance and interchromosomal. Snap leverages a combination of three insights: increasing read lengths, which allow for fast hash-based location of reads using larger "seed" sequences; increasing server memories, which allow trading memory to save cpu time (snap is designed for server machines with tens of gigabytes of ram); and a novel algorithm for set intersection, edit.
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