You’ll only go through this course one time, if you set aside a time and a place to go through each lesson. MEGAHIT v1.0: A Fast and Scalable Metagenome Assembler driven by Advanced Methodologies and Community Practices. Do not listen to tapes while driving because you must listen completely while going through this course. Li, D., Luo, R., Liu, C.M., Leung, C.M., Ting, H.F., Sadakane, K., Yamashita, H.Bioinformatics, doi: 10.1093/bioinformatics/btv033. Li, D., Liu, C-M., Luo, R., Sadakane, K., and Lam, T-W., (2015) MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.To see the full manual, run megahit without parameters or with -h.Īlso, our wiki may be helpful. -continue -o out: resume an interrupted job from out.-cleaning-rounds 1 -disconnect-ratio 0: get less pruned assembly (usually shorter contigs).-presets meta-large: if the metagenome is complex (i.e., bio-diversity is high, for example soil metagenomes).-kmin-1pass: if sequencing depth is low and too much memory used when build the graph of k_min.The contigs can be found in the output directory. Megahit_core contig2fastg 119 out/intermediate_contigs/ > k119.fastg # get FASTG from the intermediate contigs of k=119 Megahit -1 a1.fq,b1.fq,c1.fq -2 a2.fq,b2.fq,c2.fq -r se1.fq,se2.fq -o out # 3 paired-end libraries + 2 SE libraries Megahit -12 interleaved.fq -o out # one paired & interleaved paired-end library Megahit -1 pe_1.fq -2 pe_2.fq -o out # 1 paired-end library
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