scc4% smalt help
SMALT - Sequence Mapping and Alignment Tool
smalt [TASK_OPTIONS] [ ]
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 is a pairwise sequence alignment program designed for the mapping of
DNA sequencing reads onto genomic reference sequences.
Running the software involves two steps. First, an index of short words
has to be built for the set of genomic reference sequences (issue
'smalt index -H' for help). Then the sequencing reads are mapped onto the
reference ('smalt map -H' for help).