第一步是组装 第二步是得到一致性序列 #! /bin/sh ~/usr/wtdbg2-master/wtdbg2 -t 16 -x sq -g 370m -i ../data/pb.fasta.gz -fo prefix ~/usr/wtdbg2-master/wtpoa-cns -t 16 -i prefix.ctg.lay.gz -fo prefix.ctg.fa -t 核数 16, -x 测序平台 PacBio Sequel, -g 基因组预估大...
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 ...
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...
With the support by the National Natural Science Foundation of China,Prof.Ruan Jue(阮珏)at the Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,developed a novel long reads assembler,which was published in Nature Methods(2020,17:155—158).中国科学基金(英文版)...
./wtdbg2 -x rs -g 4.6m -t 16 -i reads.fa.gz -fo prefix ./wtpoa-cns -t 16 -i prefix.ctg.lay.gz -fo prefix.ctg.fa where-gis the estimated genome size and-xspecifies the sequencing technology, which could take value "rs" for PacBio RSII, "sq" for PacBio Sequel, "ccs" fo...
使用HTTPS 协议时,命令行会出现如下账号密码验证步骤。基于安全考虑,Gitee 建议 配置并使用私人令牌 替代登录密码进行克隆、推送等操作 Username for 'https://gitee.com': userName Password for 'https://userName@gitee.com': # 私人令牌 wtdbg2 / wtdbg-graph.h wtdbg-graph.h 131.95 KB ...
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...
static inline int dna_cmpx_seqs(u8i *seqs, u8i seq_size){ register int i, j; register u1i a, b; j = (seq_size + 1) >> 1; for(i=0;i<j;i++){ a = bits2bit(seqs, i); b = (~bits2bit(seqs, seq_size - 1 - i)) & 0x03U; if(a < b) return -1; ...
git clone https://github.com/ruanjue/wtdbg2 cd wtdbg2 && 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 ...
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...