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