HISAT supports genomes of any size, including those larger than 4 billion bases. It employs two types of indexes for alignment: (1) a whole-genome FM index to anchor each alignment,Īnd (2) numerous local FM indexes for very rapid extensions of these alignments. Which is inherently well-suited for aligning across introns. HISAT uses a novel indexing scheme, hierarchical indexing, HISAT is a highly efficient system for aligning RNA-seq reads. Which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. TopHat-Fusion is an enhanced version of TopHat with the ability to align reads across fusion points, TopHat2 includes TopHat-Fusion as an option. The last release, TopHat2, runs with either Bowtie1 or Bowtie2 and includes algorithms that significant enhance TopHat's sensitivity, particularly in the presence of pseudogenes. TopHat finds known and novelĮxon-exon splice junctions and is extremely fast due to its use of the Bowtie2 aligner. Bowtie and Bowtie2 were developed by Ben LangmeadĪ spliced alignment system for RNA-seq experiments. Genome with a Burrows-Wheeler index to keep its memory footprint small:Ģ.3 GB for the human genome. Sequences to the human genome at a rate of about 25 million reads per With high throughput (~1.5 to 2 million reads per second with the human reference genome in a 4-GPU computer), it is well suited to large-scale NGS data processing.Īn ultrafast, memory-efficient short read aligner that aligns short DNA Next-generation sequence alignment softwareĪrioc is a GPU-accelerated DNA short-read aligner for WGS and WGBS reads. If you're looking for the CHESS human gene database, it is at /chess Genome Assembly and Large-Scale Genome alignment.Metagenomics Classification, Abundance Estimation and Visualization.Next-Generation Sequence Alignment Software.
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