Haplotype-aware de novo assembly. Collapsed assembly approaches identify sequence variants on a consensus assembly and subsequently phase these variants into haplotypes using chromosome-scale data (Hi-C). Semi-collapsed approaches follow a similar approach, but after phasing, variants in the initial asse...
Inbred animals were historically chosen for genome analysis to circumvent assembly issues caused by haplotype variation but this resulted in a composite of the two genomes. Here we report a haplotype-aware scaffolding and polishing pipeline which was used to create haplotype-resolved, chromosome-level ...
Third-generation nanopore sequence data have demonstrated a long read length, but current interpretation methods for their novel pore-based signal have unique error profiles, making accurate analysis challenging. Here, we introduce a haplotype-aware variant calling pipeline, PEPPER-Margin-DeepVariant, ...
Other parameters are optional. Please runpython phasebook.py -hto get details of optional parameters setting. The final polished haplotype aware contigs are included in thecontigs.fafile under output directory. Before running phasebook, please read through the following basic parameter settings, which...
A haplotype-aware de novo assembly of related individuals using pedigree sequence graph. Bioinformatics. 2020;36:2385–92. 13. Koren S, et al. De novo assembly of haplotype-resolved genomes with trio binning. Nat Biotechnol. 2018;36:1174–82. 14. Garg S, et al. Chromosome-scale, ...
[37]. This bloom filter is used to filter out singleton k-mers when counting all k-mers. -r Rounds of haplotype-aware error corrections [3]. This option affects all outputs of hifiasm\_meta. --min-hist-cnt When analyzing the k-mer spectrum, ignore counts below INT [5]. # Assembly ...
A haplotype-aware de novo assembly of related individuals using pedigree sequence graph. Bioinformatics. 2020;36:2385–92. 13. Koren S, et al. De novo assembly of haplotype-resolved genomes with trio binning. Nat Biotechnol. 2018;36:1174–82. 14. Garg S, et al. Chromosome-scale, ...
we integrate a suite of cutting-edge genomic technologies that, when used collectively, allow SVs to be comprehensively assessed in a haplotype-aware manner in diploid genomes. In addition, we also identify the optimal combination of technologies and algorithms that would maximize sensitivity and speci...
RNA-seq reads from six tissues (root, stem, flower, bud, young leaves and mature leaves) were generated using three biological replicates. RNA-seq reads were trimmed using the Trimmomatic56program and mapped against allele-aware annotated gene models using Bowtie57with only the best alignment ret...
(https://www.pacb.com/support/software-downloads/) were used to polish these contigs by realigning the SMRT reads. The Pbmm2 alignment used the parameter -j 108 -preset SUBREAD, and gcpp polish used the parameter -j 96. Pilon (v1.22)59was used for further error correction by aligning ...