HISAT2-Teaching - Revision history

Shtsai at 00:48, 5 April 2026

2026-04-05T00:48:18Z

← Older revision		Revision as of 20:48, 4 April 2026
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	[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Teaching		Teaching

	=== Version ===		== Version ==
	2.2.1		2.2.1

	=== Author / Distributor ===		== Author / Distributor ==

	[https://ccb.jhu.edu/software/hisat2/index.shtml HISAT2]		[https://ccb.jhu.edu/software/hisat2/index.shtml HISAT2]

	=== Description ===		== Description ==
	"HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome)."		"HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome)."
	More details are at [https://ccb.jhu.edu/software/hisat2/index.shtml HISAT2]		More details are at [https://ccb.jhu.edu/software/hisat2/index.shtml HISAT2]

	=== Running Program ===		== Running Program ==
	<!--		<!--
	The last version of this application is at /apps/eb/HISAT2/3n-20201216-gompi-2022a		The last version of this application is at /apps/eb/HISAT2/3n-20201216-gompi-2022a
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==

	<pre class="gcommand">		<pre class="gcommand">
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	Source code is obtained from [https://ccb.jhu.edu/software/hisat2/index.shtml HISAT2]		Source code is obtained from [https://ccb.jhu.edu/software/hisat2/index.shtml HISAT2]

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Shtsai: /* Version */

2026-01-09T19:39:57Z

Version

← Older revision		Revision as of 15:39, 9 January 2026
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	=== Version ===		=== Version ===
	2.2.1~~, 3~~		2.2.1

	=== Author / Distributor ===		=== Author / Distributor ===

Shtsai: /* Running Program */

2026-01-09T19:39:38Z

Running Program

← Older revision		Revision as of 15:39, 9 January 2026
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	=== Running Program ===		=== Running Program ===
			<!--
	The last version of this application is at /apps/eb/HISAT2/3n-20201216-gompi-2022a		The last version of this application is at /apps/eb/HISAT2/3n-20201216-gompi-2022a

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	ml HISAT2/3n-20201216-gompi-2022a		ml HISAT2/3n-20201216-gompi-2022a
	</pre>		</pre>
			-->
	To use version 2.2.1, please load the module with		To use version 2.2.1, please load the module with
	<pre class="gscript">		<pre class="gscript">

Chelsea: /* Version */

2024-05-09T17:15:09Z

Version

← Older revision		Revision as of 13:15, 9 May 2024
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	=== Version ===		=== Version ===
	2.2.1		2.2.1, 3

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	The last version of this application is at /apps/eb/HISAT2/~~2.2.1~~-gompi-2022a		The last version of this application is at /apps/eb/HISAT2/3n-20201216-gompi-2022a

	To use this version, please load the module with		To use this version, please load the module with<pre class="gscript">
			ml HISAT2/3n-20201216-gompi-2022a
			</pre>

			To use version 2.2.1, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml HISAT2/2.2.1-gompi-2022a		ml HISAT2/2.2.1-gompi-2022a

Shtsai at 18:43, 6 September 2023

2023-09-06T18:43:06Z

← Older revision		Revision as of 14:43, 6 September 2023
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	=== Version ===		=== Version ===
	2.1.0		2.2.1

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	The last version of this application is at /apps/eb/HISAT2/2.1.0-~~foss~~-~~2019b~~		The last version of this application is at /apps/eb/HISAT2/2.2.1-gompi-2022a

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml HISAT2/2.1.0-~~foss~~-~~2019b~~		ml HISAT2/2.2.1-gompi-2022a
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml HISAT2/2.1.0-~~foss~~-~~2019b~~<br>		ml HISAT2/2.2.1-gompi-2022a<br>
	hisat2 <u>[options]</u><br>		hisat2 <u>[options]</u><br>
	</div>		</div>
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	<pre class="gcommand">		<pre class="gcommand">
	ml HISAT2/2.1.0-~~foss~~-~~2019b~~		ml HISAT2/2.2.1-gompi-2022a
	hisat2 -help		hisat2 -help
	HISAT2 version 2.1.0 by Daehwan Kim (infphilo@gmail.com, www.ccb.jhu.edu/people/infphilo)
			HISAT2 version 2.2.1 by Daehwan Kim (infphilo@gmail.com, www.ccb.jhu.edu/people/infphilo)
	Usage:		Usage:
	hisat2 [options]* -x <ht2-idx> {-1 <m1> -2 <m2> \| -U <r> \| --sra-acc <SRA accession number>} [-S <sam>]		hisat2 [options]* -x <ht2-idx> {-1 <m1> -2 <m2> \| -U <r> \| --sra-acc <SRA accession number>} [-S <sam>]
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	--int-quals qualities encoded as space-delimited integers		--int-quals qualities encoded as space-delimited integers
	--sra-acc SRA accession ID		--sra-acc SRA accession ID

			Presets: Same as:
			--fast --no-repeat-index
			--sensitive --bowtie2-dp 1 -k 30 --score-min L,0,-0.5
			--very-sensitive --bowtie2-dp 2 -k 50 --score-min L,0,-1

	Alignment:		Alignment:
			--bowtie2-dp <int> use Bowtie2's dynamic programming alignment algorithm (0) - 0: no dynamic programming, 1: conditional dynamic programming, and 2: unconditional dynamic programming (slowest)
	--n-ceil <func> func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)		--n-ceil <func> func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
	--ignore-quals treat all quality values as 30 on Phred scale (off)		--ignore-quals treat all quality values as 30 on Phred scale (off)
	--nofw do not align forward (original) version of read (off)		--nofw do not align forward (original) version of read (off)
	--norc do not align reverse-complement version of read (off)		--norc do not align reverse-complement version of read (off)
			--no-repeat-index do not use repeat index

	Spliced Alignment:		Spliced Alignment:
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	--dta reports alignments tailored for transcript assemblers		--dta reports alignments tailored for transcript assemblers
	--dta-cufflinks reports alignments tailored specifically for cufflinks		--dta-cufflinks reports alignments tailored specifically for cufflinks
	--avoid-pseudogene tries to avoid aligning reads to pseudogenes (experimental option)�		--avoid-pseudogene tries to avoid aligning reads to pseudogenes (experimental option)
	--no-templatelen-adjustment disables template length adjustment for RNA-seq reads		--no-templatelen-adjustment disables template length adjustment for RNA-seq reads

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	Reporting:		Reporting:
	-k <int> (~~default~~: 5) ~~report up~~ to <int> ~~alns per~~ read		-k <int> It searches for at most <int> distinct, primary alignments for each read. Primary alignments mean
			alignments whose alignment score is equal to or higher than any other alignments. The search terminates
			when it cannot find more distinct valid alignments, or when it finds <int>, whichever happens first.
			The alignment score for a paired-end alignment equals the sum of the alignment scores of
			the individual mates. Each reported read or pair alignment beyond the first has the SAM ‘secondary’ bit
			(which equals 256) set in its FLAGS field. For reads that have more than <int> distinct,
			valid alignments, hisat2 does not guarantee that the <int> alignments reported are the best possible
			in terms of alignment score. Default: 5 (linear index) or 10 (graph index).
			Note: HISAT2 is not designed with large values for -k in mind, and when aligning reads to long,
			repetitive genomes, large -k could make alignment much slower.
			--max-seeds <int> HISAT2, like other aligners, uses seed-and-extend approaches. HISAT2 tries to extend seeds to
			full-length alignments. In HISAT2, --max-seeds is used to control the maximum number of seeds that
			will be extended. For DNA-read alignment (--no-spliced-alignment), HISAT2 extends up to these many seeds
			and skips the rest of the seeds. For RNA-read alignment, HISAT2 skips extending seeds and reports
			no alignments if the number of seeds is larger than the number specified with the option,
			to be compatible with previous versions of HISAT2. Large values for --max-seeds may improve alignment
			sensitivity, but HISAT2 is not designed with large values for --max-seeds in mind, and when aligning
			reads to long, repetitive genomes, large --max-seeds could make alignment much slower.
			The default value is the maximum of 5 and the value that comes with -k times 2.
			-a/--all HISAT2 reports all alignments it can find. Using the option is equivalent to using both --max-seeds
			and -k with the maximum value that a 64-bit signed integer can represent (9,223,372,036,854,775,807).
			--repeat report alignments to repeat sequences directly

	Paired-end:		Paired-end:
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	(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.		(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
	--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)		--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
	--summary-file print alignment summary to this file.		--summary-file <path> print alignment summary to this file.
	--new-summary print alignment summary in a new style, which is more machine-friendly.		--new-summary print alignment summary in a new style, which is more machine-friendly.
	--quiet print nothing to stderr except serious errors		--quiet print nothing to stderr except serious errors
	--met-file <path> send metrics to file at <path> (off)		--met-file <path> send metrics to file at <path> (off)
	--met-stderr send metrics to stderr (off)		--met-stderr send metrics to stderr (off)
	--met <int> report internal counters & metrics every <int> secs (1)		--met <int> report internal counters & metrics every <int> secs (1)
	--no-head ~~supppress~~ header lines, i.e. lines starting with @		--no-head suppress header lines, i.e. lines starting with @
	--no-sq ~~supppress~~ @SQ header lines		--no-sq suppress @SQ header lines
	--rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field		--rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field
	--rg <text> add <text> ("lab:value") to @RG line of SAM header.		--rg <text> add <text> ("lab:value") to @RG line of SAM header.
	Note: @RG line only printed when --rg-id is set.		Note: @RG line only printed when --rg-id is set.
	--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.		--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.

	Performance:		Performance:

Shtsai at 02:09, 28 August 2020

2020-08-28T02:09:50Z

← Older revision		Revision as of 22:09, 27 August 2020
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	=== Running Program ===		=== Running Program ===

	The last version of this application is at ~~/usr/local~~/apps/eb/HISAT2/2.1.0-foss-~~2016b~~		The last version of this application is at /apps/eb/HISAT2/2.1.0-foss-2019b

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml HISAT2/2.1.0-foss-~~2016b~~		ml HISAT2/2.1.0-foss-2019b
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml HISAT2/2.1.0-foss-~~2016b~~<br>		ml HISAT2/2.1.0-foss-2019b<br>
	hisat2 <u>[options]</u><br>		hisat2 <u>[options]</u><br>
	</div>		</div>
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	<pre class="gcommand">		<pre class="gcommand">
	ml HISAT2/2.1.0-foss-~~2016b~~		ml HISAT2/2.1.0-foss-2019b
	hisat2 -help		hisat2 -help
	HISAT2 version 2.1.0 by Daehwan Kim (infphilo@gmail.com, www.ccb.jhu.edu/people/infphilo)		HISAT2 version 2.1.0 by Daehwan Kim (infphilo@gmail.com, www.ccb.jhu.edu/people/infphilo)

Yhuang: Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 2.1.0 === A..."

2018-08-15T16:26:04Z

Created page with "Category:Teaching Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 2.1.0 === A..."

New page

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Teaching

=== Version ===
2.1.0

=== Author / Distributor ===

[https://ccb.jhu.edu/software/hisat2/index.shtml HISAT2]

=== Description ===
"HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome)."
More details are at [https://ccb.jhu.edu/software/hisat2/index.shtml HISAT2]

=== Running Program ===

The last version of this application is at /usr/local/apps/eb/HISAT2/2.1.0-foss-2016b

To use this version, please load the module with
<pre class="gscript">
ml HISAT2/2.1.0-foss-2016b
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_HISAT2 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=HISAT2.%j.out 
<nowiki>#</nowiki>SBATCH --error=HISAT2.%j.err 

cd $SLURM_SUBMIT_DIR 
ml HISAT2/2.1.0-foss-2016b 
hisat2 [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml HISAT2/2.1.0-foss-2016b
hisat2 -help
HISAT2 version 2.1.0 by Daehwan Kim (infphilo@gmail.com, www.ccb.jhu.edu/people/infphilo)
Usage:
hisat2 [options]* -x <ht2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <sam>]

<ht2-idx> Index filename prefix (minus trailing .X.ht2).
<m1> Files with #1 mates, paired with files in <m2>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<m2> Files with #2 mates, paired with files in <m1>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<r> Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<SRA accession number> Comma-separated list of SRA accession numbers, e.g. --sra-acc SRR353653,SRR353654.
<sam> File for SAM output (default: stdout)

<m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):

Input:
-q query input files are FASTQ .fq/.fastq (default)
--qseq query input files are in Illumina's qseq format
-f query input files are (multi-)FASTA .fa/.mfa
-r query input files are raw one-sequence-per-line
-c <m1>, <m2>, <r> are sequences themselves, not files
-s/--skip <int> skip the first <int> reads/pairs in the input (none)
-u/--upto <int> stop after first <int> reads/pairs (no limit)
-5/--trim5 <int> trim <int> bases from 5'/left end of reads (0)
-3/--trim3 <int> trim <int> bases from 3'/right end of reads (0)
--phred33 qualities are Phred+33 (default)
--phred64 qualities are Phred+64
--int-quals qualities encoded as space-delimited integers
--sra-acc SRA accession ID

Alignment:
--n-ceil <func> func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
--ignore-quals treat all quality values as 30 on Phred scale (off)
--nofw do not align forward (original) version of read (off)
--norc do not align reverse-complement version of read (off)

Spliced Alignment:
--pen-cansplice <int> penalty for a canonical splice site (0)
--pen-noncansplice <int> penalty for a non-canonical splice site (12)
--pen-canintronlen <func> penalty for long introns (G,-8,1) with canonical splice sites
--pen-noncanintronlen <func> penalty for long introns (G,-8,1) with noncanonical splice sites
--min-intronlen <int> minimum intron length (20)
--max-intronlen <int> maximum intron length (500000)
--known-splicesite-infile <path> provide a list of known splice sites
--novel-splicesite-outfile <path> report a list of splice sites
--novel-splicesite-infile <path> provide a list of novel splice sites
--no-temp-splicesite disable the use of splice sites found
--no-spliced-alignment disable spliced alignment
--rna-strandness <string> specify strand-specific information (unstranded)
--tmo reports only those alignments within known transcriptome
--dta reports alignments tailored for transcript assemblers
--dta-cufflinks reports alignments tailored specifically for cufflinks
--avoid-pseudogene tries to avoid aligning reads to pseudogenes (experimental option)�
--no-templatelen-adjustment disables template length adjustment for RNA-seq reads

Scoring:
--mp <int>,<int> max and min penalties for mismatch; lower qual = lower penalty <6,2>
--sp <int>,<int> max and min penalties for soft-clipping; lower qual = lower penalty <2,1>
--no-softclip no soft-clipping
--np <int> penalty for non-A/C/G/Ts in read/ref (1)
--rdg <int>,<int> read gap open, extend penalties (5,3)
--rfg <int>,<int> reference gap open, extend penalties (5,3)
--score-min <func> min acceptable alignment score w/r/t read length
(L,0.0,-0.2)

Reporting:
-k <int> (default: 5) report up to <int> alns per read

Paired-end:
-I/--minins <int> minimum fragment length (0), only valid with --no-spliced-alignment
-X/--maxins <int> maximum fragment length (500), only valid with --no-spliced-alignment
--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
--no-mixed suppress unpaired alignments for paired reads
--no-discordant suppress discordant alignments for paired reads

Output:
-t/--time print wall-clock time taken by search phases
--un <path> write unpaired reads that didn't align to <path>
--al <path> write unpaired reads that aligned at least once to <path>
--un-conc <path> write pairs that didn't align concordantly to <path>
--al-conc <path> write pairs that aligned concordantly at least once to <path>
(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
--summary-file print alignment summary to this file.
--new-summary print alignment summary in a new style, which is more machine-friendly.
--quiet print nothing to stderr except serious errors
--met-file <path> send metrics to file at <path> (off)
--met-stderr send metrics to stderr (off)
--met <int> report internal counters & metrics every <int> secs (1)
--no-head supppress header lines, i.e. lines starting with @
--no-sq supppress @SQ header lines
--rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field
--rg <text> add <text> ("lab:value") to @RG line of SAM header.
Note: @RG line only printed when --rg-id is set.
--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.

Performance:
-o/--offrate <int> override offrate of index; must be >= index's offrate
-p/--threads <int> number of alignment threads to launch (1)
--reorder force SAM output order to match order of input reads
--mm use memory-mapped I/O for index; many 'hisat2's can share

Other:
--qc-filter filter out reads that are bad according to QSEQ filter
--seed <int> seed for random number generator (0)
--non-deterministic seed rand. gen. arbitrarily instead of using read attributes
--remove-chrname remove 'chr' from reference names in alignment
--add-chrname add 'chr' to reference names in alignment
--version print version information and quit
-h/--help print this usage message

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [https://ccb.jhu.edu/software/hisat2/index.shtml HISAT2]

=== System ===
64-bit Linux