Parallelism: The best way to optimize sirFAST is to split the reads into chunks that fit into the memory of the cluster nodes. The number of reads is approximately ((M-600)/(4*L)) mil where M is the size of the memory for the cluster node(MB) and L is the read length. If you have more nodes, you can make the chunks smaller to use the nodes efficiently. For example, if the library length is 50bp and the memory of nodes is 2GIG, chunks should (2000-600)/(4*50)= 7mil reads.
To see the list of options, use "-h" or "--help".
To see the current version of sirFAST, user "-v" or "--version".
$./sirFAST --index refgen.fasta
Upon the completion of the indexing phase, you can find "refgen.fasta.index" in the same directory as "refgen.fasta".
The indexing done in sirFAST depends on the read format you are using. We use 10 and 9 for read format 5-10-10-10 and read format 10-9-N-10 respectively.
$./sirsfast --search refgen.fa --seq reads.tsv
The reported locations will be saved into "output" by default. If you want to save it somewhere else, use "-o" to specify another file. sirFAST can report the unmapped reads in fasta/fastq format.
$./sirFAST --search refgen.fasta --seq reads.tsv -o my.map
The number of the mismatches allowed by sirFAST is 2 by default. You can modify this number by using "-e". There is no best mapping option in sirFAST.
$./sirFAST --search refgen.fasta --seq reads.tsv -e 3
To map paired-end reads, use "--pe" option. The mapping can be done in single/batch mode. If the reads are in two different files, you have to use "--seq1/--seq2" to indicate the files. If the reads are interleaved, use "--seq" to indicated the file. The distance allowed between the paired-end reads should be specified with "--min" and "--max". "--min" and "--max" specify the minmum and maximum of the inferred size (the distance between outer edges of the mapping mates).
$./sirFAST --search refgen.fasta --pe --seq reads.tsv --min 150 --max 250
$./sirFAST -b --search index.list --pe --seq1 reads1.tsv --seq2 reads2.tsv --min 50 --max 75
sirFAST can report the discordant mapping for use of Variation Hunter (Work In Progress.). The --min and --max optiopns will define the minimum and maximum inferred size for concordant mapping.
$./sirFAST --search refgen.fasta --pe --discordant-vh --seq reads.tsv --min 50 --max 75
Donghyuk Lee, Farhad Hormozdiari, Hongyi Xin, Faraz Hach, Onur Mutlu, and Can Alkan,
"Fast and Accurate Mapping of Complete Genomics Reads" Methods, October 22, 2014.