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 unstable Mon Sep  4 12:49:40 UTC 2017 Compiler: gcc version 7.2.0
       (Ubuntu 7.2.0-12ubuntu1) 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}