De novo genome assembly reconstructs the chromosomes from massive relatively short fragmented reads and serves as fundamental for studying new species where there is no reference genome. Wtdbg2 is a ...doi:10.1007/978-3-030-60245-1_16Dun, Ming...
git clone https://github.com/ruanjue/wtdbg2cdwtdbg2&&make#assemble long reads./wtdbg2 -x rs -g 4.6m -i reads.fa.gz -t16 -fo prefix#derive consensus./wtpoa-cns -t16 -i prefix.ctg.lay.gz -fo prefix.ctg.fa#polish consensus, not necessary if you want to polish the assemblies using...
Data Sourcehttp://datasets.pacb.com/2014/Human54x/fasta.html Command wtdbg2 -t 96 -i pb.fa -fo dbg --tidy-reads 5000 --edge-min 2 --rescue-low-cov-edges ContigsTOT 2978536704, CNT 8752, AVG 340327, MAX 11662848, N50 1925120, L50 453, N90 400128, L90 1727, Min 5120 ...
//static inline TriPOG* init_tripog(u4i seqmax, int refmode, int winlen, int winmin, int fail_skip, int M, int X, int I, int D, int W, int use_sse, int rW, u4i min_cnt, float min_freq){ static inline TriPOG* init_tripog(u4i seqmax, int shuffle, int winlen, int ...
g[(h - j) * (w +1) + x] ='|'; } } returng; } staticinlinechar*barplot_txt_u8_simple(u4i w, u4i h, u8i *vals, u4i size, u8i max_val){ char*g; doublehdiv; u8i wdiv; u4i i, j, x, y; g =malloc((w +1) * h +1); ...
git clone https://github.com/ruanjue/wtdbg2cdwtdbg2&&make#assemble long reads./wtdbg2 -x rs -g 4.6m -i reads.fa.gz -t16 -fo prefix#derive consensus./wtpoa-cns -t16 -i prefix.ctg.lay.gz -fo prefix.ctg.fa#polish consensus, not necessary if you want to polish the assemblies using...
git clone https://github.com/ruanjue/wtdbg2cdwtdbg2&&make#quick start with wtdbg2.pl./wtdbg2.pl -t 16 -x rs -g 4.6m -o dbg reads.fa.gz#Step by step commandlines#assemble long reads./wtdbg2 -x rs -g 4.6m -i reads.fa.gz -t 16 -fo dbg#derive consensus./wtpoa-cns -t 16...