misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads

Zhu, Xiao; Leung, Ho-fung; Wang, Rongjie; Chin, Francis Y. L.; Yiu, Siu Ming; Quan, Guangri; Li, Yajie; Zhang, Rui; Jiang, Qinghua; Liu, Bo; Dong, Yucui; Zhou, Guohui; Wang, Yadong

doi:10.1186/s12859-015-0818-3

Cited by 16 publications

(8 citation statements)

References 31 publications

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“…Generating the BAM file is done prior to, and independent of, the functionality of PACVr and can be conducted under a series of different settings, which may be reflected in the resulting visualization. For example, users may wish to visualize coverage depth calculated only from sequence reads that map to the reference genome as concordant read pairs, which can be beneficial in the identification of assembly errors [68]. Similarly, users may wish to visualize coverage depth calculated only from sequence reads that map to more than one location in the reference genome, which, if applied to plastid genomes, typically highlights the location of the IRs.…”

Section: Input and Output Specificationsmentioning

confidence: 99%

PACVr: plastome assembly coverage visualization in R

2020

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Background: Plastid genomes typically display a circular, quadripartite structure with two inverted repeat regions, which challenges automatic assembly procedures. The correct assembly of plastid genomes is a prerequisite for the validity of subsequent analyses on genome structure and evolution. The average coverage depth of a genome assembly is often used as an indicator of assembly quality. Visualizing coverage depth across a draft genome is a critical step, which allows users to inspect the quality of the assembly and, where applicable, identify regions of reduced assembly confidence. Despite the interplay between genome structure and assembly quality, no contemporary, user-friendly software tool can visualize the coverage depth of a plastid genome assembly while taking its quadripartite genome structure into account. A software tool is needed that fills this void. Results: We introduce 'PACVr', an R package that visualizes the coverage depth of a plastid genome assembly in relation to the circular, quadripartite structure of the genome as well as the individual plastome genes. By using a variable window approach, the tool allows visualizations on different calculation scales. It also confirms sequence equality of, as well as visualizes gene synteny between, the inverted repeat regions of the input genome. As a tool for plastid genomics, PACVr provides the functionality to identify regions of coverage depth above or below user-defined threshold values and helps to identify non-identical IR regions. To allow easy integration into bioinformatic workflows, PACVr can be invoked from a Unix shell, facilitating its use in automated quality control. We illustrate the application of PACVr on four empirical datasets and compare visualizations generated by PACVr with those of alternative software tools. Conclusions: PACVr provides a user-friendly tool to visualize (a) the coverage depth of a plastid genome assembly on a circular, quadripartite plastome map and in relation to individual plastome genes, and (b) gene synteny across the inverted repeat regions. It contributes to optimizing plastid genome assemblies and increasing the reliability of publicly available plastome sequences. The software, example datasets, technical

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Section: Input and Output Specificationsmentioning

confidence: 99%

PACVr: plastome assembly coverage visualization in R

2020

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“…Tools such as Pilon [20] and REAPR [21] perform misassembly correction using short reads, and others such as misFinder [22] additionally use a closely-related reference genome. While ReMILO [23] can use long reads in its assembly correction pipeline, it does not use this evidence exclusively, but in addition to short-read data and a reference genome.…”

Section: Introductionmentioning

confidence: 99%

LongStitch: High-quality genome assembly correction and scaffolding using long reads

Coombe

et al. 2021

Preprint

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Background Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information. Long reads are better able to span repetitive genomic regions compared to short reads, and thus have tremendous utility for resolving problematic regions and helping generate more complete draft assemblies. Here, we present LongStitch, a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads. Results LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively, previously developed for linked reads, that we adapted for long reads. Here, we describe the LongStitch pipeline and introduce our new long-read scaffolder, ntLink, which utilizes lightweight minimizer mappings to join contigs. LongStitch was tested on short and long-read assemblies of three different human individuals using corresponding nanopore long-read data, and improves the contiguity of each assembly from 2.0-fold up to 304.6-fold (as measured by NGA50 length). Furthermore, LongStitch generates more contiguous and correct assemblies compared to state-of-the-art long-read scaffolder LRScaf in most tests, and consistently runs in under five hours using less than 23GB of RAM. Conclusions Due to its effectiveness and efficiency in improving draft assemblies using long reads, we expect LongStitch to benefit a wide variety of de novo genome assembly projects. The LongStitch pipeline is freely available at https://github.com/bcgsc/longstitch.

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“…While existing mis-assembly detection methods (e.g. QUAST [ 20 ], REAPR [ 21 ], misFinder [ 22 ]) require the reads used in genome assembly and/or a reference sequence, GC skew can indicate a potential mis-assembly from the genome sequence alone.…”

Section: Introductionmentioning

confidence: 99%

SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes

Salzberg

2020

PLoS Comput Biol

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GC skew is a phenomenon observed in many bacterial genomes, wherein the two replication strands of the same chromosome contain different proportions of guanine and cytosine nucleotides. Here we demonstrate that this phenomenon, which was first discovered in the mid-1990s, can be used today as an analysis tool for the 15,000+ complete bacterial genomes in NCBI’s Refseq library. In order to analyze all 15,000+ genomes, we introduce a new method, SkewIT (Skew Index Test), that calculates a single metric representing the degree of GC skew for a genome. Using this metric, we demonstrate how GC skew patterns are conserved within certain bacterial phyla, e.g. Firmicutes, but show different patterns in other phylogenetic groups such as Actinobacteria. We also discovered that outlier values of SkewIT highlight potential bacterial mis-assemblies. Using our newly defined metric, we identify multiple mis-assembled chromosomal sequences in previously published complete bacterial genomes. We provide a SkewIT web app https://jenniferlu717.shinyapps.io/SkewIT/ that calculates SkewI for any user-provided bacterial sequence. The web app also provides an interactive interface for the data generated in this paper, allowing users to further investigate the SkewI values and thresholds of the Refseq-97 complete bacterial genomes. Individual scripts for analysis of bacterial genomes are provided in the following repository: https://github.com/jenniferlu717/SkewIT.

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misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads

Cited by 16 publications

References 31 publications

PACVr: plastome assembly coverage visualization in R

PACVr: plastome assembly coverage visualization in R

LongStitch: High-quality genome assembly correction and scaffolding using long reads

SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes

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