micro-read Fast Alignment Search Tool
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README.md

mrfast

micro-read Fast Alignment Search Tool

mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 4+4 bp. This manual, describes how to choose the parameters and tune mrFAST with respect to the library settings. mrFAST is designed to find 'all' mappings for a given set of reads, however it can return one "best" map location if the relevant parameter is invoked.

NOTE: mrFAST is developed for Illumina, thus requires all reads to be at the same length. For paired-end reads, lengths of mates may be different from each other, but each "side" should have a uniform length.

mrFAST : Micro-Read Fast Alignment Search Tool. Enhanced with FastHASH.

Usage:

mrfast [options]

General Options:

-v|--version    Current Version.  
-h    Shows the help file.  

Indexing Options:

--index [file]    Generate an index from the specified fasta file.   
--ws [int]    Set window size for indexing (default:12 max:14).  

Searching Options:

--search [file]    Search in the specified genome. Provide the path to the fasta file. Index file should be in the same directory.  
--pe    Search will be done in Paired-End mode.  
--seq [file]    Input sequences in fasta/fastq format [file]. If paired end reads are interleaved, use this option.  
--seq1 [file]    Input sequences in fasta/fastq format [file] (First file). Use this option to indicate the first file of paired end reads.   
--seq2 [file]    Input sequences in fasta/fastq format [file] (Second file). Use this option to indicate the second file of paired end reads.    
-o [file]    Output of the mapped sequences. The default is "output".  
-u [file]    Save unmapped sequences in fasta/fastq format.  
--best    Only the best mapping from all the possible mapping is returned.  
--seqcomp    Indicates that the input sequences are compressed (gz).  
--outcomp    Indicates that output file should be compressed (gz).  
-e [int]    Maximum allowed edit distance (default 4% of the read length).  
--min [int]    Min distance allowed between a pair of end sequences.  
--max [int]    Max distance allowed between a pair of end sequences.  
--maxoea [int]    Max number of One End Anchored (OEA) returned for each read pair. We recommend 100 or above for NovelSeq use. Default = 100.	
--maxdis [int]    Max number of discordant map locations returned for each read pair. We recommend 300 or above for VariationHunter use. Default = 300.  
--crop [int]    Trim the reads to the given length.  
--sample [string]    Sample name to be added to the SAM header (optional).  
--rg [string]    Read group ID to be added to the SAM header (optional).  
--lib [string]    Library name to be added to the SAM header (optional).