Provided by: hisat2_2.1.0-2_amd64 bug


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


       HISAT2 version 2.1.0 by Daehwan Kim (,

              hisat2-align [options]* -x <ht2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]

              Index filename prefix (minus trailing .X.ht2l).

       <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):


       -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)

              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)

       --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

              disable the use of splice sites found

              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

              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

              print alignment summary to this file.

              print alignment summary in a new style, which is more machine-friendly.

              print nothing to stderr except serious errors

       --met-file <path>
              send metrics to file at <path> (off)

              send metrics to stderr (off)

       --met <int>
              report internal counters & metrics every <int> secs (1)

              supppress header lines, i.e. lines starting with @

              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

       --mm   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  (Ubuntu
       8.2.0-9ubuntu1)  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,