Version 2.04: released on July 13th, 2012 Compile Jul 9 2013 11:57:16 ******************** Pregraph ******************** Parameters: pregraph pregraph -s configFile -o outputGraph [-R] [-K kmer -p n_cpu -a initMemoryAssumption -d KmerFreqCutoff] -s configFile: the config file of solexa reads -o outputGraph: prefix of output graph file name -K kmer(min 13, max 63): kmer size, [23] -p n_cpu: number of cpu for use, [8] -a initMemoryAssumption: memory assumption initialized to avoid further reallocation, unit GB, [0] -R (optional) output extra information for resolving repeats in contig step, [NO] -d KmerFreqCutoff: kmers with frequency no larger than KmerFreqCutoff will be deleted, [0] Version 2.04: released on July 13th, 2012 Compile Jul 9 2013 11:57:16 Usage: sparse_pregraph -s configFile -K kmer -z genomeSize -o outputGraph [-g maxKmerEdgeLength -d kmerFreqCutoff -e kmerEdgeFreqCutoff -R -r runMode -p n_cpu] -s configFile: the config file of solexa reads -K kmer(min 13, max 63): kmer size, [23] -g maxKmerEdgeLength(min 1, max 25): number of skipped intermediate kmers, [15] -z genomeSize(required): estimated genome size -d kmerFreqCutoff: delete kmers with frequency no larger than,[1] -e kmerEdgeFreqCutoff: delete kmers' related edge with frequency no larger than [1] -R (optional) output extra information for resolving repeats in contig step, [NO] -r runMode: 0 build graph & build edge and preArc, 1 load graph by prefix & build edge and preArc, 2 build graph only, 3 build edges only, 4 build preArcs only [0] -p n_cpu: number of cpu for use,[8] -o outputGraph: prefix of output graph file name Version 2.04: released on July 13th, 2012 Compile Jul 9 2013 11:57:16 ******************** Contig ******************** Parameters: contig contig -g InputGraph [-R] [-M mergeLevel -D EdgeCovCutoff] [-s readsInfoFile -m maxkmer -p n_cpu -r] -g inputGraph: prefix of input graph file names -R (optional) resolve repeats using information generated in pregraph step, works only if -R is set in pregraph step too, [NO] -M mergeLevel(min 0, max 3): the strength of merging similar sequences during contiging, [1] -D EdgeCovCutoff: edges shorter than (2*K+1) with coverage no larger than EdgeCovCutoff will be deleted, [1] -e arcWeight: two edges, between which the arc's weight is larger than arcWeight, will be linerized, [0] -m max k when using multi-kmer, and the parameters below are used along with multi-kmer, [NO] -s readsInfoFile:The file contains information of solexa reads(It's necessary when using multi-kmer) -p number of cpu, [8] -E (optional) merge clean bubble before iterate, works only if -M is set when using multi-kmer, [NO] Version 2.04: released on July 13th, 2012 Compile Jul 9 2013 11:57:16 ******************** Map ******************** Parameters: map map -s configFile -g inputGraph [-f] [-p n_cpu -k kmer_R2C] -s configFile: the config file of solexa reads -g inputGraph: prefix of input graph file names -f (optional) output gap related reads in map step for using SRkgf to fill gap, [NO] -p n_cpu: number of cpu for use, [8] -k kmer_R2C(min 13, max 63): kmer size used for mapping read to contig, [K] Version 2.04: released on July 13th, 2012 Compile Jul 9 2013 11:57:16 ******************** Scaff ******************** Parameters: scaff scaff -g inputGraph [-F -z -u -S -w] [-G gapLenDiff -L minContigLen -c minContigCvg -C maxContigCvg -b insertSizeUpperBound -B bubbleCoverage -N genomeSize -p n_cpu] -g inputGraph: prefix of input graph file names -F (optional) fill gaps in scaffold, [No] -z (optional) use compatible mode to build scaffold with contig produced by Version 1.05, [No] -u (optional) un-mask contigs with high/low coverage before scaffolding, [mask] -S (optional) if scaffold structure exists, do gapfilling only(-F), [NO] -w (optional) keep contigs weakly connected to other contigs in scaffold, [NO] -V (optional) output information for Hawkeye to visualize the assembly, [NO] -G gapLenDiff: allowed length difference between estimated and filled gap, [50] -L minContigLen: shortest contig for scaffolding, [K+2] -c minContigCvg: minimum contig coverage (c*avgCvg), contigs shorter than 100bp with coverage smaller than c*avgCvg will be masked before scaffolding unless -u is set, [0.1] -C maxContigCvg: maximum contig coverage (C*avgCvg), contigs with coverage larger than C*avgCvg or contigs shorter than 100bp with coverage larger than 0.8*C*avgCvg will be masked before scaffolding unless -u is set, [2] -b insertSizeUpperBound: (b*avg_ins) will be used as upper bound of insert size for large insert size ( > 1000) when handling pair-end connections between contigs if b is set to larger than 1, [1.5] -B bubbleCoverage: remove contig with lower cvoerage in bubble structure if both contigs' coverage are smaller than bubbleCoverage*avgCvg, [0.6] -N genomeSize: genome size for statistics, [0] -p n_cpu: number of cpu for use, [8] Version 2.04: released on July 13th, 2012 Compile Jul 9 2013 11:57:16 SOAPdenovo all -s configFile -o outputGraph [-R -F -u -w] [-K kmer -p n_cpu -a initMemoryAssumption -d KmerFreqCutOff -D EdgeCovCutoff -M mergeLevel -k kmer_R2C, -G gapLenDiff -L minContigLen -c minContigCvg -C maxContigCvg -b insertSizeUpperBound -B bubbleCoverage -N genomeSize] -s configFile: the config file of solexa reads -o outputGraph: prefix of output graph file name -K kmer(min 13, max 63): kmer size, [23] -p n_cpu: number of cpu for use, [8] -a initMemoryAssumption: memory assumption initialized to avoid further reallocation, unit G, [0] -d kmerFreqCutoff: kmers with frequency no larger than KmerFreqCutoff will be deleted, [0] -R (optional) resolve repeats by reads, [NO] -D edgeCovCutoff: edges with coverage no larger than EdgeCovCutoff will be deleted, [1] -M mergeLevel(min 0, max 3): the strength of merging similar sequences during contiging, [1] -e arcWeight: two edges, between which the arc's weight is larger than arcWeight, will be linerized, [0] -m maxKmer (max 63): maximum kmer size used for multi-kmer, [NO] -E (optional) merge clean bubble before iterate, works only if -M is set when using multi-kmer, [NO] -k kmer_R2C(min 13, max 63): kmer size used for mapping reads to contigs, [K] -F (optional) fill gaps in scaffolds, [NO] -u (optional) un-mask contigs with high/low coverage before scaffolding, [mask] -w (optional) keep contigs weakly connected to other contigs in scaffold, [NO] -G gapLenDiff: allowed length difference between estimated and filled gap, [50] -L minContigLen: shortest contig for scaffolding, [K+2] -c minContigCvg: minimum contig coverage (c*avgCvg), contigs shorter than 100bp with coverage smaller than c*avgCvg will be masked before scaffolding unless -u is set, [0.1] -C maxContigCvg: maximum contig coverage (C*avgCvg), contigs with coverage larger than C*avgCvg or contigs shorter than 100bp with coverage larger than 0.8*C*avgCvg will be masked before scaffolding unless -u is set, [2] -b insertSizeUpperBound: (b*avg_ins) will be used as upper bound of insert size for large insert size ( > 1000) when handling pair-end connections between contigs if b is set to larger than 1, [1.5] -B bubbleCoverage: remove contig with lower cvoerage in bubble structure if both contigs' coverage are smaller than bubbleCoverage*avgCvg, [0.6] -N genomeSize: genome size for statistics, [0] -V (optional) output information for Hawkeye to visualize the assembly, [NO]