Phased Assembly Variant Caller. PAV is a tool for discovering variation using assembled genomes aligned to a reference. It supports both phased and unphased assemblies. PAV was developed for the Human Genome Structural Variation Consortium (HGSVC)

2023年11月22日 · 染色体结构变异（Structure Variation, SV），指基因组上发生的长度大于50bp的大片段插入 (Insertion, INS)、缺失 (Deletion, DEL)、倒位 (Inversion, INV)、易位 (Translocation)、重复（Duplication, DUP）等类型的变异，其中占比最大的就是大片段的插入和缺失（图1）。 插入缺失很好理解就是，多了一段或者少了一段DNA序列；重复就是有一段区域的序列重复出现；倒位就是序列翻转了一下，如本来那个位置该是AATTG的，结果变成 …

此外还有基于长测序读长（Long Reads，LR）、针对一些特定插入突变（MEI/NUMT/VEI）和其他类型的分析方法： LR: PBHoney-NGM，pbsv，Sniffles MEI/NUMT/VEI： ITIS，MELT，Mobster，RetroSeq，Tangram，Tea，TEMP，BatVI，HGT-ID，VirusFinder2，VirusSeq

2023年1月17日 · Long-read sequencing has demonstrated great potential for characterizing all types of structural variations (SVs). However, existing algorithms have insufficient sensitivity and precision. To...

2018年3月28日 · One way to determine the completeness of an assembly is by detecting its Presence–Absence variations (PAV) with respect to a reference, where PAVs between two assemblies are defined as the sequences present in one assembly but entirely missing in …

2023年5月17日 · Long-read sequencing technologies, such as Pacific Bioscience (PacBio) and Oxford Nanopore Technology (ONT), have emerged as superior to short-read sequencing for SV detection and thus reveal a number of novel SV functional impacts missed by short-read data .

2020年3月5日 · Here we analyze the association of gene PAV with resistance of oilseed rape (Brassica napus) against the important fungal pathogen Verticillium longisporum, as an example for a complex,...

2021年8月20日 · In this study, we discover and characterize several megabase-scale presence-absence variations (PAVs) in the maize genome. Surprisingly, we identify a 3.2 Mb PAV fragment that shows high integrity and is present as complete presence …

2022年5月5日 · Haplotype-phased assemblies (Data and Code Availability) were used to generate a long-read-based inversion callset, using the PAV (Ebert et al., 2021) tool, and these assemblies were further utilized to perform sequence-level characterization of inverted sequences. PAV was run on 32/44 samples (64/88 haplotypes) with available phased assemblies.

2023年10月20日 · Presence/absence variation (PAV) is a well-known phenomenon in prokaryotes that was described for the first time in bivalves in 2020 in Mytilus galloprovincialis. The objective of the present study was to further our understanding of the PAV phenomenon in mussel biology.