NAME

       smalt - Sequence Mapping and Alignment Tool

DESCRIPTION

       SMALT  efficiently  aligns  DNA  sequencing reads with a reference genome.  It Reads from a wide range of
       sequencing platforms, for example  Illumina,  Roche-454,  Ion  Torrent,  PacBio  or  ABI-Sanger,  can  be
       processed including paired reads.

       The  software employs a perfect hash index of short words (< 20 nucleotides long), sampled at equidistant
       steps along the genomic reference sequences.

       For each read, potentially matching segments in the reference are identified from  seed  matches  in  the
       index and subsequently aligned with the read using a banded Smith-Waterman algorithm.

       The  best  gapped  alignments  of each read is reported including a score for the reliability of the best
       mapping. The user can adjust the trade-off between sensitivity and speed by tuning the length and spacing
       of the hashed words.

       A  mode  for  the  detection  of split (chimeric) reads is provided.  Multi-threaded program execution is
       supported.

SYNOPSIS

       smalt <task> [TASK_OPTIONS] [<index_name> <file_name_A> [<file_name_B>]]

   Available tasks:
       smalt check
              - checks FASTA/FASTQ input

       smalt help
              - prints a brief summary of this software

       smalt index
              - builds an index of k-mer words for the reference

       smalt map
              - maps single or paired reads onto the reference

       smalt sample
              - sample insert sizes for paired reads

              smalt version - prints version information

   Help on individual tasks:
              smalt <task> -H