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What is HISAT2 index?
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.
How long does it take to index a genome?
Max reads: 100000 Set genome to 1 Loaded Reference: 5.117 seconds. Loading index for chunk 1-8, build 1 Generated Index: 10.184 seconds. Analyzed Index: 11.591 seconds.
What is a genome index?
Indexing a genome can be explained similar to indexing a book. If you want to know on which page a certain word appears or a chapter begins, it is much more efficient/faster to look it up in a pre-built index than going through every page of the book until you found it. Same goes for alignments.
How long do stars take map?
Last time I mapped my data with STAR that took me less than two minutes. But this time for 0.1 percent of data it took 45 minutes to map !!! The only differences are these : data size already mapped was 290 MB (on virtual box ubuntu).
How many GFM indexes do you need for HISAT2?
In addition to using one global GFM index that represents general population, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover human population).
How to build a HFM Index in GTF?
Depend on your purpose, you have to download reference sequence, gene annotation and SNP files. We also provides scripts to build indexes. Download Download GTF and make exon, splicesite file. If you want to build HFM index, you can skip this step. If you want to build HFM index, you can skip this step.
Where are large indexes stored in HISAT2 build?
When the genome is longer, hisat2-build builds a “large” index using 64-bit numbers. Small indexes are stored in files with the .ht2 extension, and large indexes are stored in files with the .ht2l extension.
What kind of alignment program is HISAT2 for?
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as against a single reference genome).