Provided by: hisat2_2.2.1-4_amd64 bug

NAME

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

DESCRIPTION

       HISAT2 version 2.2.1 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

       Presets:
              Same as:

       --fast                 --no-repeat-index

       --sensitive            --bowtie2-dp 1 -k 30 --score-min L,0,-0.5

       --very-sensitive       --bowtie2-dp 2 -k 50 --score-min L,0,-1

              Alignment:

       --bowtie2-dp <int> use Bowtie2's dynamic programming  alignment  algorithm  (0)  -  0:  no
              dynamic  programming,  1:  conditional  dynamic  programming,  and 2: unconditional
              dynamic programming (slowest)

       --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)

       --no-repeat-index
              do not use repeat index

              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>
              It searches for at most <int> distinct, primary alignments for each  read.  Primary
              alignments  mean  alignments  whose  alignment score is equal to or higher than any
              other alignments. The search terminates when it cannot  find  more  distinct  valid
              alignments,  or  when it finds <int>, whichever happens first.  The alignment score
              for a paired-end alignment equals the sum of the alignment scores of the individual
              mates.  Each  reported  read  or  pair  alignment  beyond  the  first  has  the SAM
              ???secondary??? bit (which equals 256) set in its FLAGS field. For reads that  have
              more  than  <int>  distinct,  valid  alignments, hisat2 does not guarantee that the
              <int> alignments reported are the  best  possible  in  terms  of  alignment  score.
              Default:  5  (linear index) or 10 (graph index).  Note: HISAT2 is not designed with
              large values for -k in mind, and when aligning reads to long,  repetitive  genomes,
              large -k could make alignment much slower.

       --max-seeds <int>
              HISAT2,  like  other  aligners,  uses  seed-and-extend  approaches. HISAT2 tries to
              extend seeds to full-length alignments. In HISAT2, --max-seeds is used  to  control
              the  maximum  number  of  seeds  that  will  be  extended.  For  DNA-read alignment
              (--no-spliced-alignment), HISAT2 extends up to these many seeds and skips the  rest
              of  the  seeds. For RNA-read alignment, HISAT2 skips extending seeds and reports no
              alignments if the number of seeds is larger than  the  number  specified  with  the
              option,  to  be  compatible  with  previous  versions  of  HISAT2. Large values for
              --max-seeds may improve alignment sensitivity, but  HISAT2  is  not  designed  with
              large  values  for --max-seeds in mind, and when aligning reads to long, repetitive
              genomes, large --max-seeds could make alignment much slower.  The default value  is
              the maximum of 5 and the value that comes with -k times 2.

       -a/--all
              HISAT2  reports all alignments it can find. Using the option is equivalent to using
              both --max-seeds and -k with the maximum value that a  64-bit  signed  integer  can
              represent (9,223,372,036,854,775,807).

       --repeat
              report alignments to repeat sequences directly

              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 <path> 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
              suppress header lines, i.e. lines starting with @

       --no-sq
              suppress @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  14  October  2022  Compiler:   gcc   version   12.2.0   (Ubuntu
       12.2.0-9ubuntu1)   Options:   -O3    -funroll-loops  -g3  -Wdate-time  -D_FORTIFY_SOURCE=2
       -std=c++11 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}