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

NAME

hisat2-align-s - HISAT2 graph-based alignment of short nucleotide reads to many genomes, small index binary

DESCRIPTION

HISAT2 version 2.1.0 by Daehwan Kim (infphilo@gmail.com, www.ccb.jhu.edu/people/infphilo) Usage:
hisat2-align [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>.
<m2>
Files with #2 mates, paired with files in <m1>.
<r>
Files with unpaired reads.
<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
--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}

September 2018 hisat2-align-s version 2.1.0