This is the command smalt that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
Use smalt online using onworks.net services
