SureMap is composed of an index builder and an aligner. The package can be download here: SureMap. Currently, it is tested on 64 bit Linux.

The index builder can be used as follows:

(at least 48GB RAM is required for building index files of human genome)

usage: ./SureMap-IndexBuilder     <input.fasta>     <outputFolder>
example: ./SureMap-IndexBuilder     /path/to/reference/genome/hg19.fa      /some-path/

The aligner can be called as:

(at least 9GB RAM is required for mapping reads to the human genome)

usage: ./SureMap-Aligner      [OPTIONS]      <ref.fa>        <query file>
ref.fa: the indexed reference genome
query file: reads in fastq format
OPTIONS:
-a report all locations [default : disabled]
-b report bestOne  [default : disabled]
-g map with  indels [default : disabled]
-u report only unique alignments [default : disabled]
-t val[int]  number of threads [default : 1]
-k val[int]  maximum number of alignments to be reported for each read [default : 1]
-e val[double] estimated error rate of reads [default : 0.05]
-v val[int] maximum number of allowed mismatch (included gap if any) for read mapping
-o val[string]  output sam file [defaul : report.sam]
-m val[string] choose sensitivity threshold {fast, normal, sensitive, very-sensitive}[default: normal]
EXAMPLE : ./SureMap-Aligner   -t 2    -u    -e 0.1    -o output.sam    -m fast    /path/to/index/directory/hg19.fa       query.fastq