Provided by: hisat2_2.1.0-4_amd64 
NAME
hisat2-align-s - graph-based alignment of short nucleotide reads to many genomes, wrapper
script
DESCRIPTION
HISAT2 version 2.1.0 by Daehwan Kim (infphilo@gmail.com, www.ccb.jhu.edu/people/infphilo)
Usage:
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 11 February 2020 Compiler: gcc version 9.2.1 20200203 (Ubuntu
9.2.1-28ubuntu1) Options: -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 Sizeof
{int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}