.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.
.TH HISAT2-ALIGN-S "1" "September 2018" "hisat2-align-s version 2.1.0" "User Commands"
.SH NAME
hisat2-align-s \- graph-based alignment of short nucleotide reads to many genomes, wrapper script
.SH DESCRIPTION
HISAT2 version 2.1.0 by Daehwan Kim (infphilo@gmail.com, www.ccb.jhu.edu/people/infphilo)
Usage:
.IP
hisat2 [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.ht2).
.TP
<m1>
Files with #1 mates, paired with files in <m2>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
.TP
<m2>
Files with #2 mates, paired with files in <m1>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
.TP
<r>
Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
.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
.IP
Alignment:
.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)
.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:
.HP
\fB\-k\fR <int> (default: 5) report up to <int> alns per read
.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
.TP
\fB\-\-un\fR <path>
write unpaired reads that didn't align to <path>
.TP
\fB\-\-al\fR <path>
write unpaired reads that aligned at least once to <path>
.TP
\fB\-\-un\-conc\fR <path>
write pairs that didn't align concordantly to <path>
.TP
\fB\-\-al\-conc\fR <path>
write pairs that aligned concordantly at least once to <path>
.IP
(Note: for \fB\-\-un\fR, \fB\-\-al\fR, \fB\-\-un\-conc\fR, or \fB\-\-al\-conc\fR, add '\-gz' to the option name, e.g.
\fB\-\-un\-gz\fR <path>, to gzip compress output, or add '\-bz2' to bzip2 compress output.)
\fB\-\-summary\-file\fR     print alignment summary to this file.
\fB\-\-new\-summary\fR      print alignment summary in a new style, which is more machine\-friendly.
\fB\-\-quiet\fR            print nothing to stderr except serious errors
\fB\-\-met\-file\fR <path>  send metrics to file at <path> (off)
\fB\-\-met\-stderr\fR       send metrics to stderr (off)
\fB\-\-met\fR <int>        report internal counters & metrics every <int> secs (1)
\fB\-\-no\-head\fR          supppress header lines, i.e. lines starting with @
\fB\-\-no\-sq\fR            supppress @SQ header lines
\fB\-\-rg\-id\fR <text>     set read group id, reflected in @RG line and RG:Z: opt field
\fB\-\-rg\fR <text>        add <text> ("lab:value") to @RG line of SAM header.
.IP
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
24 September 2018
Compiler: gcc version 8.2.0 (Debian 8.2.0\-7)
Options: \fB\-O3\fR   \fB\-funroll\-loops\fR \fB\-g3\fR \fB\-Wdate\-time\fR \fB\-D_FORTIFY_SOURCE\fR=\fI\,2\/\fR \fB\-DPOPCNT_CAPABILITY\fR
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}