.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH HISAT2-ALIGN-L "1" "August 2023" "hisat2-align-l version 2.2.1" "User Commands"
.SH NAME
hisat2-align-l \- HISAT2 graph-based alignment of short nucleotide reads to many genomes, large index binary
.SH DESCRIPTION
HISAT2 version 2.2.1 by Daehwan Kim (infphilo@gmail.com, www.ccb.jhu.edu/people/infphilo)
Usage:
.IP
hisat2\-align [options]* \fB\-x\fR <ht2\-idx> {\-1 <m1> \fB\-2\fR <m2> | \fB\-U\fR <r>} [\-S <sam>]
.TP
<ht2\-idx>
Index filename prefix (minus trailing .X.ht2l).
.TP
<m1>
Files with #1 mates, paired with files in <m2>.
.TP
<m2>
Files with #2 mates, paired with files in <m1>.
.TP
<r>
Files with unpaired reads.
.TP
<sam>
File for SAM output (default: stdout)
.IP
<m1>, <m2>, <r> can be comma\-separated lists (no whitespace) and can be
specified many times.  E.g. '\-U file1.fq,file2.fq \fB\-U\fR file3.fq'.
.PP
Options (defaults in parentheses):
.IP
Input:
.TP
\fB\-q\fR
query input files are FASTQ .fq/.fastq (default)
.TP
\fB\-\-qseq\fR
query input files are in Illumina's qseq format
.TP
\fB\-f\fR
query input files are (multi\-)FASTA .fa/.mfa
.TP
\fB\-r\fR
query input files are raw one\-sequence\-per\-line
.TP
\fB\-c\fR
<m1>, <m2>, <r> are sequences themselves, not files
.TP
\fB\-s\fR/\-\-skip <int>
skip the first <int> reads/pairs in the input (none)
.TP
\fB\-u\fR/\-\-upto <int>
stop after first <int> reads/pairs (no limit)
.TP
\fB\-5\fR/\-\-trim5 <int>
trim <int> bases from 5'/left end of reads (0)
.TP
\fB\-3\fR/\-\-trim3 <int>
trim <int> bases from 3'/right end of reads (0)
.TP
\fB\-\-phred33\fR
qualities are Phred+33 (default)
.TP
\fB\-\-phred64\fR
qualities are Phred+64
.TP
\fB\-\-int\-quals\fR
qualities encoded as space\-delimited integers
.TP
Presets:
Same as:
.HP
\fB\-\-fast\fR                 \fB\-\-no\-repeat\-index\fR
.HP
\fB\-\-sensitive\fR            \fB\-\-bowtie2\-dp\fR 1 \fB\-k\fR 30 \fB\-\-score\-min\fR L,0,\-0.5
.HP
\fB\-\-very\-sensitive\fR       \fB\-\-bowtie2\-dp\fR 2 \fB\-k\fR 50 \fB\-\-score\-min\fR L,0,\-1
.IP
Alignment:
.HP
\fB\-\-bowtie2\-dp\fR <int> use Bowtie2's dynamic programming alignment algorithm (0) \- 0: no dynamic programming, 1: conditional dynamic programming, and 2: unconditional dynamic programming (slowest)
.TP
\fB\-\-n\-ceil\fR <func>
func for max # non\-A/C/G/Ts permitted in aln (L,0,0.15)
.TP
\fB\-\-ignore\-quals\fR
treat all quality values as 30 on Phred scale (off)
.TP
\fB\-\-nofw\fR
do not align forward (original) version of read (off)
.TP
\fB\-\-norc\fR
do not align reverse\-complement version of read (off)
.TP
\fB\-\-no\-repeat\-index\fR
do not use repeat index
.IP
Spliced Alignment:
.TP
\fB\-\-pen\-cansplice\fR <int>
penalty for a canonical splice site (0)
.TP
\fB\-\-pen\-noncansplice\fR <int>
penalty for a non\-canonical splice site (12)
.TP
\fB\-\-pen\-canintronlen\fR <func>
penalty for long introns (G,\-8,1) with canonical splice sites
.TP
\fB\-\-pen\-noncanintronlen\fR <func>
penalty for long introns (G,\-8,1) with noncanonical splice sites
.TP
\fB\-\-min\-intronlen\fR <int>
minimum intron length (20)
.TP
\fB\-\-max\-intronlen\fR <int>
maximum intron length (500000)
.TP
\fB\-\-known\-splicesite\-infile\fR <path>
provide a list of known splice sites
.TP
\fB\-\-novel\-splicesite\-outfile\fR <path>
report a list of splice sites
.TP
\fB\-\-novel\-splicesite\-infile\fR <path>
provide a list of novel splice sites
.TP
\fB\-\-no\-temp\-splicesite\fR
disable the use of splice sites found
.TP
\fB\-\-no\-spliced\-alignment\fR
disable spliced alignment
.TP
\fB\-\-rna\-strandness\fR <string>
specify strand\-specific information (unstranded)
.TP
\fB\-\-tmo\fR
reports only those alignments within known transcriptome
.TP
\fB\-\-dta\fR
reports alignments tailored for transcript assemblers
.TP
\fB\-\-dta\-cufflinks\fR
reports alignments tailored specifically for cufflinks
.TP
\fB\-\-avoid\-pseudogene\fR
tries to avoid aligning reads to pseudogenes (experimental option)
.TP
\fB\-\-no\-templatelen\-adjustment\fR
disables template length adjustment for RNA\-seq reads
.IP
Scoring:
.TP
\fB\-\-mp\fR <int>,<int>
max and min penalties for mismatch; lower qual = lower penalty <6,2>
.TP
\fB\-\-sp\fR <int>,<int>
max and min penalties for soft\-clipping; lower qual = lower penalty <2,1>
.TP
\fB\-\-no\-softclip\fR
no soft\-clipping
.TP
\fB\-\-np\fR <int>
penalty for non\-A/C/G/Ts in read/ref (1)
.TP
\fB\-\-rdg\fR <int>,<int>
read gap open, extend penalties (5,3)
.TP
\fB\-\-rfg\fR <int>,<int>
reference gap open, extend penalties (5,3)
.TP
\fB\-\-score\-min\fR <func> min acceptable alignment score w/r/t read length
(L,0.0,\-0.2)
.IP
Reporting:
.TP
\fB\-k\fR <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 \fB\-k\fR in mind, and when aligning reads to long,
repetitive genomes, large \fB\-k\fR could make alignment much slower.
.TP
\fB\-\-max\-seeds\fR <int>
HISAT2, like other aligners, uses seed\-and\-extend approaches. HISAT2 tries to extend seeds to
full\-length alignments. In HISAT2, \fB\-\-max\-seeds\fR is used to control the maximum number of seeds that
will be extended. For DNA\-read alignment (\fB\-\-no\-spliced\-alignment\fR), 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 \fB\-\-max\-seeds\fR may improve alignment
sensitivity, but HISAT2 is not designed with large values for \fB\-\-max\-seeds\fR in mind, and when aligning
reads to long, repetitive genomes, large \fB\-\-max\-seeds\fR could make alignment much slower.
The default value is the maximum of 5 and the value that comes with \fB\-k\fR times 2.
.TP
\fB\-a\fR/\-\-all
HISAT2 reports all alignments it can find. Using the option is equivalent to using both \fB\-\-max\-seeds\fR
and \fB\-k\fR with the maximum value that a 64\-bit signed integer can represent (9,223,372,036,854,775,807).
.TP
\fB\-\-repeat\fR
report alignments to repeat sequences directly
.IP
Paired\-end:
.TP
\fB\-I\fR/\-\-minins <int>
minimum fragment length (0), only valid with \fB\-\-no\-spliced\-alignment\fR
.TP
\fB\-X\fR/\-\-maxins <int>
maximum fragment length (500), only valid with \fB\-\-no\-spliced\-alignment\fR
.HP
\fB\-\-fr\fR/\-\-rf/\-\-ff     \fB\-1\fR, \fB\-2\fR mates align fw/rev, rev/fw, fw/fw (\fB\-\-fr\fR)
.TP
\fB\-\-no\-mixed\fR
suppress unpaired alignments for paired reads
.TP
\fB\-\-no\-discordant\fR
suppress discordant alignments for paired reads
.IP
Output:
.TP
\fB\-t\fR/\-\-time
print wall\-clock time taken by search phases
.HP
\fB\-\-summary\-file\fR <path> print alignment summary to this file.
.TP
\fB\-\-new\-summary\fR
print alignment summary in a new style, which is more machine\-friendly.
.TP
\fB\-\-quiet\fR
print nothing to stderr except serious errors
.TP
\fB\-\-met\-file\fR <path>
send metrics to file at <path> (off)
.TP
\fB\-\-met\-stderr\fR
send metrics to stderr (off)
.TP
\fB\-\-met\fR <int>
report internal counters & metrics every <int> secs (1)
.TP
\fB\-\-no\-head\fR
suppress header lines, i.e. lines starting with @
.TP
\fB\-\-no\-sq\fR
suppress @SQ header lines
.TP
\fB\-\-rg\-id\fR <text>
set read group id, reflected in @RG line and RG:Z: opt field
.TP
\fB\-\-rg\fR <text>
add <text> ("lab:value") to @RG line of SAM header.
Note: @RG line only printed when \fB\-\-rg\-id\fR is set.
.TP
\fB\-\-omit\-sec\-seq\fR
put '*' in SEQ and QUAL fields for secondary alignments.
.IP
Performance:
.HP
\fB\-o\fR/\-\-offrate <int> override offrate of index; must be >= index's offrate
.HP
\fB\-p\fR/\-\-threads <int> number of alignment threads to launch (1)
.TP
\fB\-\-reorder\fR
force SAM output order to match order of input reads
.TP
\fB\-\-mm\fR
use memory\-mapped I/O for index; many 'hisat2's can share
.IP
Other:
.TP
\fB\-\-qc\-filter\fR
filter out reads that are bad according to QSEQ filter
.TP
\fB\-\-seed\fR <int>
seed for random number generator (0)
.HP
\fB\-\-non\-deterministic\fR seed rand. gen. arbitrarily instead of using read attributes
.TP
\fB\-\-remove\-chrname\fR
remove 'chr' from reference names in alignment
.TP
\fB\-\-add\-chrname\fR
add 'chr' to reference names in alignment
.TP
\fB\-\-version\fR
print version information and quit
.TP
\fB\-h\fR/\-\-help
print this usage message
.PP
64\-bit
Built on Debian
05 August 2023
Compiler: gcc version 13.2.0 (Debian 13.2.0\-1)
Options: \fB\-O3\fR   \fB\-funroll\-loops\fR \fB\-g3\fR \fB\-Wdate\-time\fR \fB\-D_FORTIFY_SOURCE\fR=\fI\,2\/\fR \fB\-std\fR=\fI\,c\/\fR++11
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}