"An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph" "for assembling large and complex metagenomics data" http://www.ncbi.nlm.nih.gov/pubmed/25609793 Downloadhttps://github.com/voutcn/megahitExampleInput: metagenomics sample as paired-end fastq files _1 and _2./megahit -1 SAMPLE_1.fastq -2 SAMPLE_2.fastq -m 0.5 -t 12 -o megahit_result -m 0.5 use 50% of available memory (default: 90%, -m 0.9) -t 12 use 12 threads (number of parallel processors)Result: assembled contigs are in fasta file: megahit_result/final.contigs.fa Intro & Tutorialhttps://github.com/voutcn/megahithttps://github.com/voutcn/megahit/wiki/An-example-of-real-assembly Memory settingshttps://github.com/voutcn/megahit/wiki/MEGAHIT-Memory-setting Helpmegahit -h MEGAHIT v1.0.2 Copyright (c) The University of Hong Kong & L3 Bioinformatics Limited contact: Dinghua Li <dhli@cs.hku.hk> Usage: megahit [options] {-1 <pe1> -2 <pe2> | --12 <pe12> | -r <se>} [-o <out_dir>] Input options that can be specified for multiple times (supporting plain text and gz/bz2 extensions) -1 <pe1> comma-separated list of fasta/q paired-end #1 files, paired with files in <pe2> -2 <pe2> comma-separated list of fasta/q paired-end #2 files, paired with files in <pe1> --12 <pe12> comma-separated list of interleaved fasta/q paired-end files -r/--read <se> comma-separated list of fasta/q single-end filesInput options that can be specified for at most ONE time (not recommended): --input-cmd <cmd> command that outputs fasta/q reads to stdout; taken by MEGAHIT as SE reads Optional Arguments: Basic assembly options: --min-count <int> minimum multiplicity for filtering (k_min+1)-mers, default 2--k-min <int> minimum kmer size (<= 127), must be odd number, default 21--k-max <int> maximum kmer size (<= 127), must be odd number, default 99--k-step <int> increment of kmer size of each iteration (<= 28), must be even number, default 20 --k-list <int,int,..> comma-separated list of kmer size (all must be odd, in the range 15-127, increment <= 28); override `--k-min', `--k-max' and `--k-step' Advanced assembly options: --no-mercy do not add mercy kmers--no-bubble do not merge bubbles--merge-level <l,s> merge complex bubbles of length <= l*kmer_sizeand similarity >= s, default 20,0.98 --prune-level <int> strength of local low depth pruning (0-2), default 2--low-local-ratio <float> ratio threshold to define low local coveragecontigs, default 0.2 --max-tip-len <int> remove tips less than this value; default 2*k foriteration of kmer_size=k --no-local disable local assembly--kmin-1pass use 1pass mode to build SdBG of k_minPresets parameters: --presets <str> override a group of parameters; possible values: meta '--min-count 2 --k-list 21,41,61,81,99' (generic metagenomes, default) meta-sensitive '--min-count 2 --k-list 21,31,41,51,61,71,81,91,99' (more sensitive but slower) meta-large '--min-count 2 --k-list 27,37,47,57,67,77,87' (large & complex metagenomes, like soil) bulk '--min-count 3 --k-list 31,51,71,91,99 --no-mercy' (experimental, standard bulk sequencing with >= 30x depth) single-cell '--min-count 3 --k-list 21,33,55,77,99,121 --merge_level 20,0.96' (experimental, single cell data) Hardware options: -m/--memory <float> max memory in byte to be used in SdBG construction; default 0.9 (if set between 0-1, fraction of the machine's total memory) --mem-flag <int> SdBG builder memory mode, default 10: minimum; 1: moderate; others: use all memory specified by '-m/--memory'. --use-gpu use GPU--gpu-mem <float> GPU memory in byte to be used. Default: auto detect to use up all free GPU memory. -t/--num-cpu-threads <int> number of CPU threads, at least 2. Default: auto detect to use all CPU threads. Output options: -o/--out-dir <string> output directory, default ./megahit_out--out-prefix <string> output prefix (the contig file will beOUT_DIR/OUT_PREFIX.contigs.fa) --min-contig-len <int> minimum length of contigs to output, default 200--keep-tmp-files keep all temporary filesOther Arguments: --continue continue a MEGAHIT run from its last available check point.please set the output directory correctly when using this option. -h/--help print the usage message-v/--version print version--verbose verbose mode |