HISAT 2.2.1 release 7/24/2020

This patch version includes the following changes.

• Python3 support
• Remove HISAT-genotype related scripts. HISAT-genotype moved to https://daehwankimlab.github.io/hisat-genotype/
• Fixed bugs related to --read-lengths option

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HISAT 2.2.0 release 2/6/2020

This major version update includes a new feature to handle “repeat” reads. Based on sets of 100-bp simulated and 101-bp real reads that we tested, we found that 2.6-3.4% and 1.4-1.8% of the reads were mapped to >5 locations and >100 locations, respectively. Attempting to report all alignments would likely consume a prohibitive amount of disk space. In order to address this issue, our repeat indexing and alignment approach directly aligns reads to repeat sequences, resulting in one repeat alignment per read. HISAT2 provides application programming interfaces (API) for C++, Python, and JAVA that rapidly retrieve genomic locations from repeat alignments for use in downstream analyses.
Other minor bug fixes are also included as follows:

• Fixed occasional sign (+ or -) issues of template lengths in SAM file
• Fixed duplicate read alignments in SAM file
• Skip a splice site if exon’s last base or first base is ambiguous (N)

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HISAT2-2.1.0 release 6/8/2017

This major version includes the first release of HISAT-genotype, which currently performs HLA typing, DNA fingerprinting analysis, and CYP typing on whole genome sequencing (WGS) reads. We plan to extend the system so that it can analyze not just a few genes, but a whole human genome. Please refer to the HISAT-genotype website for more details.

• HISAT2 can be directly compiled and executed on Windows system using Visual Studio, thanks to Nigel Dyer.
• Implemented --new-summary option to output a new style of alignment summary, which is easier to parse for programming purposes.
• Implemented --summary-file option to output alignment summary to a file in addition to the terminal (e.g. stderr).
• Fixed discrepancy in HISAT2’s alignment summary.
• Implemented --no-templatelen-adjustment option to disable automatic template length adjustment for RNA-seq reads.

HISAT2-2.0.5 release 11/4/2016

Version 2.0.5 is a minor release with the following changes.

• Due to a policy change (HTTP to HTTPS) in using SRA data (--sra-option), users are strongly encouraged to use this version. As of 11/9/2016, NCBI will begin a permanent redirect to HTTPS, which means the previous versions of HISAT2 no longer works with --sra-acc option soon.
• Implemented -I and -X options for specifying minimum and maximum fragment lengths. The options are valid only when used with --no-spliced-alignment, which is used for the alignment of DNA-seq reads.
• Fixed some cases where reads with SNPs on their 5' ends were not properly aligned.
• Implemented --no-softclip option to disable soft-clipping.
• Implemented --max-seeds to specify the maximum number of seeds that HISAT2 will try to extend to full-length alignments (see the manual for details).