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CG_generator
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Common.c
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Makefile
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README

sirFAST Fast and Accurate Mapping of Complete Genomics Reads

sirFAST 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. sirFAST maps short reads with respect to user defined error threshold. This manual, describes how to choose the parameters and tune sirFAST with respect to the library settings. sirFAST 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: sirFAST is developed for Complete Genomics (CG), 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.


############################# Sample Set #############################

We have provided a simple test to make sure sirFAST is working on your system properly. The sample files are in the Sample_Data folder. We provide a small template reference genome (sample_genome.fa) and a small test read sets (sample_reads_e0). The sample read set is generated with no error.

The first step is to make an index of the reference genome as follows:

$>./sirfast --index Sample_Data/sample_genome.fa

The output you should see on your screen is:

Generating Index from Sample_Data/sample_genome.fa

- chr1

DONE in 0.31s!

The second step is to make an index of the reference genome as follows:

$>./sirfast --search Sample_Data/sample_genome.fa --seq Sample_Data/sample_reads_e0 -e 0 -o Sample_Data/out.sam

The output you should see on your screen is:

You can generate the .fai file using samtools. Please place it in the same directory with the index to enable SAM headers.
=== 1996 sequences are read in 0.00. (0 discarded) [Mem:323.33 M] ===
-------------------------------------------------------------------------------------------------------------
|       Seq. Name |    Loading Time |    Mapping Time | Memory Usage(M) |  Total Mappings |    Mapped reads |
-------------------------------------------------------------------------------------------------------------
|            chr1 |            0.09 |            0.03 |          328.00 |            3728 |            1996 |
-------------------------------------------------------------------------------------------------------------
=== No more reads for mapping: finishing mapping ===
Total:            0.09              0.03

Post Processing Time:               0.02 
Total Time:                         0.15
Total No. of Reads:                 1996
Total No. of Mappings:              3728
Avg No. of locations verified:         0
			

This command generates two files. One is the Sample_Data/out.sam which contains the mapping of the reads and unmapped files which containts the unmapped reads.

#############################################################################
Note: when running sirFAST with your own reference genome file, if you see a message similar to:

WARNING: Sample_Data/sample_genome.fa.fai not found, the SAM file(s) will not have a header.

this simply means that the header in the output SAM file will be missing. To fix this, you can use samtools to generate an index file:

samtools faidx sample_genome.fa
#############################################################################

#########################  General #########################

Please download the latest version from our download page and then unzip the downloaded file. Run 'make' to build sirFAST.

    sirFAST

        generates an index of the reference genome(s) and
        maps the reads to reference genome.

Requirements:

    zlib for the ability to read compressed FASTQ and write compressed SAM files.
    C compiler (sirFAST is developed with gcc versions > 4.1.2)


Building:

On Unix/Linux systems, we recommend using GNU gcc version > 4.1.2 as your compiler and type 'make' to build.
Example:

linux> make
	
gcc -c -O3 baseFAST.c -o baseFAST.o
gcc -c -O3 CommandLineParser.c -o CommandLineParser.o
gcc -c -O3 Common.c -o Common.o
gcc -c -O3 HashTable.c -o HashTable.o
gcc -c -O3 SirFAST.c -o SirFAST.o
gcc -c -O3 Output.c -o Output.o
gcc -c -O3 Reads.c -o Reads.o
gcc -c -O3 RefGenome.c -o RefGenome.o
gcc baseFAST.o CommandLineParser.o Common.o HashTable.o SirFAST.o Output.o Reads.o RefGenome.o  
	-o sirFAST -lz -lm
rm -rf *.o
	


Parallelization: The best way to optimize sirFAST is to split the reads into chunks that fit into the memory of the cluster nodes, and implement an MPI wrapper in an embarrassingly parallel fashion. There is a multi-threaded version in the works (OMP directory), but it is not fully functional yet. We recommend the following criteria to split the reads:

    Single End Mode: The number of reads should be approximately ((M-600)/(4*L)) million where M is the size of the memory for the cluster node (in megabytes) 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 2 GB, each chunk should contain (2000-600)/(4*50)= 7 million reads.
    Paired End Mode: The number of reads in each file should not exceed 1 million (500,000 pairs), however chunk size of 500,000 reads (250,000 pairs)  is recommended.



To see the list of options, use "-h" or "--help".
To see the version of sirFAST, user "-v" or "--version".

############################# Indexing #############################

sirFAST's indices can be generated in one mode (single). In single mode, sirFAST indexes a fasta file (which may contain one or more reference genomes).

By default sirFAST uses the window size of 10 characters to generate its index. Please be advised that if you do not choose the window size carefully, you will lose sensitivity.

To index a reference genome like "refgen.fasta" run the following command:

$>./sirfast --index refgen.fasta

Upon the completion of the indexing phase, you can find "refgen.fasta.index" in the same directory as "refgen.fasta". sirFAST uses a window size of 10 (default) to make the index of the genome since the CG reads are in 10+10+10+5 bp format.

############################# Mapping #############################


sirFAST can map single-end reads and paired-end reads to a reference genome. sirFAST can map in either single or batch mode. sirFAST supports tsv format native to Complete Genomics data.

############################# Single-end Reads - Single Mode #########################

To map single reads to a reference genome in single mode, run the following command. Use "--seq" to specify the input file. refgen.fa and refgen.fa.index should be in the same folder. 

$>./sirfast --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 

By default, sirFAST reports all the locations per read. If you need one "best" mapping add the "--best" parameter to the command line:

$>./sirfast --search refgen.fasta --seq reads.tsv -e 3 --best


Note that Complete Genomics generates reads in two different formats. The earlier read type generates reads of 5-10-10-10 subreads with expected gaps in between; where the second read type is in 10-9-10 structure. sirFAST supports both read types through the "-f" parameter. See below for more about read type selection.

############################# Paired-end Reads #########################

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 

############################# Discordant Mapping
sirFAST can report the discordant mapping for use of Variation Hunter ( Still on 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



############################# Parameters #############################


General Options:

      
-v|--version 	Shows the current version.                                                                                                                                       
-h 	Shows the help screen.
    

############################# Indexing Options: #########################

      
--index [file]  Generate an index from the specified fasta file.
   
############################# Searching Options: #########################

--search [file]  
	Search the specified genome. Index file should be in same directory as the fasta file.
--pe
	Search will be done in paired-end mode
--seq [file] 	Input sequences in tsv format [file]. If pairend reads are interleaved, use this option.
--seq1 [file] 	Input sequences in tsv format [file] (First file). Use this option to indicate the first file of paired-end reads
--seq2 [file] 	Input sequences in tsv format [file] (Second file). Use this option to indicate the second file of paired-end reads.
--t [int] 	Indicates the number of reads in a chunk which is used to map in each batch. This value is 
		used for the ReadSlice version of the code when the number of mapping reads is too large. We 
		split the files to chunks and map each one seperate in sequantial manner (default: 100,000 reads)
--f [int] 	Indicates the read format.
	1 --> first read format 5-10-10-10(first mate)        10-10-10-5 (second mate)
	2 --> second read format 10-9-N-10(first mate)        10-N-9-10 (second mate)
	default: 2
-o [file] 	Output of the mapped sequences (SAM format). The default is "output".
-u [file]
		FASTA/FASTQ file for the unmapped sequences. The default is "unmapped".
-e [int] 	Maximum allowed edit distance (default 4% of the read length). Note that although the current version is limited with up to 4+4 indels, it supports any number of substitution errors.
--min [int] 	Min inferred distance allowed between two pairend sequences.
--max [int] 	Max inferred distance allowed between two pairend sequences.
--discordant-vh 	To return all discordant map locations ready for the Variation Hunter program, and OEA map locations ready for the NovelSeq.
--best 	Return "best" location only (single-end mode).
--seqcomp 	Indicates that the input sequences are compressed (gz).
--outcomp 	Indicates that output file should be compressed (gz).
--maxoea [int]
	Max number of One End Anchored (OEA) returned for each read pair. Minimum of 100 is recommendded for NovelSeq use.
--maxdis [int]
	Max number of discordant map locations returned for each read pair.
--crop [int] 	Crop the input reads at position [int].
--sample [string]
	Sample name to be added to the SAM header (optional).

 


Output Files
Single-End Mode: In the single-end mode sirFAST will generate two files as specified by the "-o" and "-u" 
parameters. Default filenename if the "-o" parameter is not specified is "output"; and default filename 
for the "-u" parameter is "unmapped".

output file ("-o"):  Contains the map locations of the sequences in the specified genome in SAM 
format. sirFAST returns all possible map locations within the given edit distance ("-e") by 
default. If the "--best" parameter is invoked, then it will select one "best" location that 
has the minimum edit distance to the genome.

unmappped file ("-u"): Contains the unmapped reads in FASTQ or FASTA format, depending on the format of the input sequences.

Paired-End and Matepair Modes: In paired-end and matepair modes, sirFAST will generate a SAM 
file in the paired-end mode that will store best mapping locations while utilizing the paired-end 
span information. In addition, it will generate a DIVET file and and OEA file (SAM format). See below:

output file ("-o"):  Contains the map locations of the sequences in the specified genome in SAM format. This file will include:
			
		If a read pair can be mapped concordantly, the "best" (minimum total edit distance and minimum differential from the average span) map location for the pair.
		If the read pair can not be mapped concordantly, again, the "best" (minimum total edit distance and minimum differential from the average span) map location for the pair.

unmapped file ("-u"): Contains the orphan (both ends unmapped) reads in FASTQ or FASTA format, depending on the format of the input sequences.

output.DIVET.vh file ("-o" option changes the prefix "output"): This file includes all possible map locations for the read pairs that cannot be concordantly mapped. This file can be loaded by VariationHunter tool for structural variation discovery ( Still on progress! ).

output_OEA file: Contains the OEA (One-End-Anchored) reads (paired-end reads where only one read can be mapped to the genome). The output is in SAM format, contains the map location of read that can be mapped to the genome. The unmapped reads of an OEA read pair are not reported in separate lines; instead the sequence and quality information is given in the line that specifies the map location of the mapped read. We use optional fields NS and NQ to specify the unmapped sequence and unmapped quality information. This file can be loaded by NovelSeq tool for novel sequence discovery ( Still on progress! ), however format conversion might be required; please see the NovelSeq documentation.

NOTE: sirFAST will report many (up to 100 by default) possible map locations for the "mapped" read of OEA  
matepairs. This will generate a large file due to repeats and duplications. This file can be limited through the --maxoea parameter.



Output Format
sirFAST mapping output format is in SAM format. For detail about the definition of the fields please refer to SAM 
Manual. All locations of discordant paired-end reads will be reported 
in DIVET format as required by the VariationHunter package. Unmapped reads (or, "orphan" read pairs in the PE mode) 
will be outputted in FASTQ or FASTA format, depending on the input sequence file format.