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Program URL: http://soap.genomics.org.cn/

SOAP has been in evolution from a single alignment tool to a
tool package that provides full solution to next generation
sequencing data analysis. Currently, it consists of a new
alignment tool (SOAPaligner/soap2), a re-sequencing
consensus sequence builder (SOAPsnp), an indel finder (
SOAPindel ), a structural variation scanner ( SOAPsv ) and a
de novo short reads assembler ( SOAPdenovo ). And a
GPU-accelerated alignment tool (SOAP3/GPU) are being
implemented.

ORDER OF THINGS

	1. pregraph or sparse_pregraph
	2. contig
	3. map
	4. scaff

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~~~~~~~~~~~~~~
~            ~~
~ SOAPdenove ~~
~            ~~
~~~~~~~~~~~~~~

SOAPdenovo is a novel short-read assembly method that can
build a de novo draft assembly for the human-sized genomes.
The program is specially designed to assemble Illumina GA
short reads. It creates new opportunities for building
reference sequences and carrying out accurate analyses of
unexplored genomes in a cost effective way. Now the new
version is available. SOAPdenovo2, which has the advantage
of a new algorithm design that reduces memory consumption in
graph construction, resolves more repeat regions in contig
assembly, increases coverage and length in scaffold
construction, improves gap closing, and optimizes for large
genome.

##################
# example.config #
##################

#maximal read length
max_rd_len=100
[LIB]
#average insert size
avg_ins=200
#if sequence needs to be reversed
reverse_seq=0
#in which part(s) the reads are used
asm_flags=3
#use only first 100 bps of each read
rd_len_cutoff=100
#in which order the reads are used while scaffolding
rank=1
# cutoff of pair number for a reliable connection (at least 3 for short insert size)
pair_num_cutoff=3
#minimum aligned length to contigs for a reliable read location (at least 32 for short insert size)
map_len=32
#a pair of fastq file, read 1 file should always be followed by read 2 file
q1=/path/**LIBNAMEA**/fastq1_read_1.fq
q2=/path/**LIBNAMEA**/fastq1_read_2.fq
#another pair of fastq file, read 1 file should always be followed by read 2 file
q1=/path/**LIBNAMEA**/fastq2_read_1.fq
q2=/path/**LIBNAMEA**/fastq2_read_2.fq
#a pair of fasta file, read 1 file should always be followed by read 2 file
f1=/path/**LIBNAMEA**/fasta1_read_1.fa
f2=/path/**LIBNAMEA**/fasta1_read_2.fa
#another pair of fasta file, read 1 file should always be followed by read 2 file
f1=/path/**LIBNAMEA**/fasta2_read_1.fa
f2=/path/**LIBNAMEA**/fasta2_read_2.fa
#fastq file for single reads
q=/path/**LIBNAMEA**/fastq1_read_single.fq
#another fastq file for single reads
q=/path/**LIBNAMEA**/fastq2_read_single.fq
#fasta file for single reads
f=/path/**LIBNAMEA**/fasta1_read_single.fa
#another fasta file for single reads
f=/path/**LIBNAMEA**/fasta2_read_single.fa
#a single fasta file for paired reads
p=/path/**LIBNAMEA**/pairs1_in_one_file.fa
#another single fasta file for paired reads
p=/path/**LIBNAMEA**/pairs2_in_one_file.fa
#bam file for single or paired reads, reads 1 in paired reads file should always be followed by reads 2
#   NOTE: If a read in bam file fails platform/vendor quality checks(the flag field 0x0200 is set), itself and it's paired 
read would be ignored.
b=/path/**LIBNAMEA**/reads1_in_file.bam
#another bam file for single or paired reads
b=/path/**LIBNAMEA**/reads2_in_file.bam
[LIB]
avg_ins=2000
reverse_seq=1
asm_flags=2
rank=2
# cutoff of pair number for a reliable connection (at least 5 for large insert size)
pair_num_cutoff=5
#minimum aligned length to contigs for a reliable read location (at least 35 for large insert size)
map_len=35
q1=/path/**LIBNAMEB**/fastq_read_1.fq
q2=/path/**LIBNAMEB**/fastq_read_2.fq
f1=/path/**LIBNAMEA**/fasta_read_1.fa
f2=/path/**LIBNAMEA**/fasta_read_2.fa
p=/path/**LIBNAMEA**/pairs_in_one_file.fa
b=/path/**LIBNAMEA**/reads_in_file.bam

#########################
# Example command lines #
#########################

$ SOAPdenovo-63mer all -s my.config -o graphOutput -K 63 -k 63 -p 32 -a 16 -d 1 -R -D 1 -M 1 -e 0 -z 9000000000 1>soap.log 2>soap.err