通过PacBio Sequel和Illumina HiSeq X Ten测序平台共获得300×单分子实时(SMRT)长度reads,107×覆盖率的illumina双末端测序reads,400×10X Genomics reads(Fig.1a、Table S1)。红脂大小蠹基因组被组装成1144个contigs,大小为320.96Mb,contig N50的长度为985.47 kb(Table 1、Table S2)。使用10X Genomics的数据改善这...
Each haplotype-specific contig-level assembly was indexed with bwa index (with -a bwtsw) (v.0.7.15-r1140)48and samtools faidx. The haplotype-specific Hi-C read pairs were aligned using bwa aln and bwa sampe. Aligned reads (in pairs) were converted into BAM files using samtools vie...
Most assemblers use graphs internally to produce their assemblies, but users often ignore the graph in favour of the conceptually simpler FASTA file of contigs. When a genome assembly is 100% complete, we have one contig per chromosome/plasmid and there's no real need for the graph. But most...
Here, we present the chromosome-level genome assembly of E. tirucalli using PacBio HiFi sequencing and Hi-C technology. Its genome size was approximately 745.62 Mb, with a contig N50 of 74.16 Mb. A total of 743.63 Mb (99.73%) of the assembled sequences were anchored to 10 ...
quinquecirrha genome assembly is highly fragmented. Here, we used the most advanced high-throughput chromosome conformation capture (Hi-C) technology to obtain high-coverage sequencing data of the C. quinquecirrha genome. We then anchored these data to the previously published contig-level assembly ...
Though it may seem that this should have been performed during the contig-generating phase, filling scaffolded gaps is often easier because there is more information available—both the size of the gap and “anchoring” contigs on both sides of it, rather than just one side. There are also ...
The key steps in the Nanopore implementation of the pipeline are carried out using theARTIC Network's field bioinformatics pipelineand were inspired by the amazing work carried out by contributors to theconnor-lab/ncov2019-artic-nf pipelineoriginally written byMatt Bullfor use by theCOG-UKproject....
(Table S2). The total length of the assembly was 605.2 Mb, with contig N50 and scaffold N50 sizes of 3.96 and 35.95 Mb, respectively (Table1). Based on the Hi-C interaction maps (Fig. S1), 582.7 (96.28%) Mb of the scaffold was anchored onto 12 chromosomes (Fig.1a and Table S3)...
The graphic assembly ofV. chinshanensemitogenome.A.The graphic mitogenome consists of three contigs with different lengths, and they connected to each other. The length of the three contigs are 330,402 bp, 263,665 bp, and 24,952 bp, respectively. Contig 3 is the potential repetitive sequenc...
a cuboid having a plurality of grids in the three dimensional space, wherein the cuboid encompasses the plurality of metagenomic sequences; and traversing progressively the plurality of grids to assemble the plurality of metagenomic sequences into one or more contigs, wherein a contig includes metag...