Main Tool: SMALT – A new mapper for DNA sequencing reads
Full documentation: https://www.sanger.ac.uk/tool/smalt-0/
SMALT aligns DNA sequencing reads with a reference genome.
This cointainer also contains samtools=1.15 as this was needed for a particular workflow. Also, bambamc=0.0.50 was added which allows passing of bam files to smalt see documentation.
SMALT - Sequence Mapping and Alignment Tool
(version: 0.7.6)
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
smalt index -k 13 -s 6 PhiX174 GCF_000819615.1_ViralProj14015_genomic.fastq
The output of this line are PhiX174.sma and PhiX174.smi. These are found in the tests directory and are included for testing the docker container during building and aren't needed to run smalt.