使用Purge Haplotigs软件从初始组装中去除冗余的序列,获得非冗余的基因组组装。使用fragScaff软件(版本140324)通过 10X Genomics linked-read data形成的super-scaffold对获得的contigs进行拼接,然后基于PacBio读取的reads,使用PBJelly软件进行间隙闭合。最后,使用Pilon v1.22软件,结合Illumina读取的短序列来纠正基因组组装中...
A system of assembling a scaffold frame without separate fasteners or clamps has slots (17) in the uprights (15) and profiled tags (18) at the ends of the horizontal sections (16). The tags protrude above the upper level of the horizontal sections and are inserted into the slot by a ...
Scaffold boundaries marked by gray vertical lines. b, Density of annotated gene models. c, Gene collinearity with barley (cv. ‘Morex’), with the position on the ‘Morex’ pseudomolecules on the vertical axis. Text and point colors represent barley chromosomes as labeled. d–g, Positions ...
and most of the reads had alotof errors. So Unicycler was designed to use low-depth and low-accuracy long reads to scaffold a short-read assembly graph to completion, an approach I call short-read-first hybrid assembly. Assuming the short-read assembly graph is in good shape, Unicycler doe...
The primary pseudohaplotype is highly contiguous, with scaffold N50 of 132 Mbp and contig N50 of 5 Mbp. The QV of 38 indicates a fairly high base-level accuracy, although somewhat below the VGP target of 4015. Table 2 Assembly quality metrics. Full size table The curated primary assembly ...
For example, a basic “greedy” assembler can start with a read and iteratively extend both ends of this read by scanning through all other reads and concatenating the ones that overlap perfectly, yielding a complete scaffold when there are no more overlapping reads. This is easy to write and...
The present work aimed using Oligopaint FISH probes to mapR. tarandusgenome scaffolds physically onto chromosomes and thereby updating a scaffold-level assembly proposed previously [20]. To our knowledge, this technology has not yet been used to assess scaffold validity or map chromosomes in mammals...
(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)...
This technique, also known as nucleated assembly, uses a single-stranded DNA as a molecular scaffold and employs multiple small staple strands to fold the scaffold into an addressable shape. An early example was described in 1999 for computational purposes and was prototyped as 2D barcode lattices...
Since the scaffolding module relies on the diploid structure of an assembly, it is not compatible with the --haploid option; we recommend the YaHS standalone scaffolder for such cases. Polyploid scaffolding and phasing is not supported yet. Consensus for user-provided paths: If you already have...