NAME¶

DESCRIPTION¶

hisat2 [options]* -x <ht2-idx> {-1 <m1> -2 <m2> | -U <r>} [-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).

<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

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

64-bit Built on Debian 24 September 2018 Compiler: gcc version 8.2.0 (Debian 8.2.0-7) Options: -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DPOPCNT_CAPABILITY Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}