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HISAT2-ALIGN-S(1) User Commands HISAT2-ALIGN-S(1)


hisat2-align-s - graph-based alignment of short nucleotide reads to many genomes, wrapper script


HISAT2 version 2.1.0 by Daehwan Kim (, Usage:
hisat2 [options]* -x <ht2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]
Index filename prefix (minus trailing .X.ht2).
Files with #1 mates, paired with files in <m2>. Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
Files with #2 mates, paired with files in <m1>. Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
Files with unpaired reads. Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
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):

query input files are FASTQ .fq/.fastq (default)
query input files are in Illumina's qseq format
query input files are (multi-)FASTA .fa/.mfa
query input files are raw one-sequence-per-line
<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)
qualities are Phred+33 (default)
qualities are Phred+64
qualities encoded as space-delimited integers
--n-ceil <func>
func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
treat all quality values as 30 on Phred scale (off)
do not align forward (original) version of read (off)
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
disable the use of splice sites found
disable spliced alignment
--rna-strandness <string>
specify strand-specific information (unstranded)
reports only those alignments within known transcriptome
reports alignments tailored for transcript assemblers
reports alignments tailored specifically for cufflinks
tries to avoid aligning reads to pseudogenes (experimental option)?
disables template length adjustment for RNA-seq reads
--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 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

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

-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)

suppress unpaired alignments for paired reads
suppress discordant alignments for paired reads
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.
put '*' in SEQ and QUAL fields for secondary alignments.

-o/--offrate <int> override offrate of index; must be >= index's offrate

-p/--threads <int> number of alignment threads to launch (1)

force SAM output order to match order of input reads
use memory-mapped I/O for index; many 'hisat2's can share
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 'chr' from reference names in alignment
add 'chr' to reference names in alignment
print version information and quit
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}

September 2018 hisat2-align-s version 2.1.0