Megadepth: efficient coverage quantification for BigWigs and BAMs

Wilks, Christopher; Ahmed, Omar; Baker, David; Zhang, David; Collado‐Torres, Leonardo; Langmead, Ben

doi:10.1101/2020.12.17.423317

Cited by 6 publications

(10 citation statements)

References 12 publications

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“…Sequencing reads were mapped against ARS-UCD1.2 with minimap2 (version 2.19-r1059-dirty) (Li, 2018). Coverage depth was determined by megadepth (version 1.1.0c) (Wilks et al, 2021), and averages over 10 Kb windows were estimated with pyBigWig (version 0.3.18) (Ramírez et al, 2016).…”

Section: Methodsmentioning

confidence: 99%

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

Leonard

Crysnanto

Fang

et al. 2021

Preprint

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Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Ten haplotype-resolved assemblies of three bovine trios representing increasing levels of heterozygosity were generated that each demonstrate a substantial improvement in contiguity and accuracy over the current Bos taurus reference genome, with more telomere and centromere content and an average 2.5x increase in NG50 and 11x decrease in base errors. Downsampling analysis demonstrated that diploid coverage as low as 20x for HiFi or 60x for ONT was sufficient to produce two haplotype-resolved assemblies meeting the standards set by the Vertebrate Genome Project. The assemblies were integrated into structural variant-based pangenomes that demonstrated significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identified approximately 900 structural variants overlapping with coding sequences; this approach revealed variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46 and GC that have potential to affect phenotype.

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Section: Methodsmentioning

confidence: 99%

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

Leonard

Crysnanto

Fang

et al. 2021

Preprint

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“…Previous methods to detect aberrant splicing have often focused on up-regulated novel junctions that are never or very rarely present in controls 15,18 . However, studies have demonstrated that splicing disruptions have complex consequences, which can be difficult to predict from DNA sequence data alone 31 . For this reason, we first explored the consequences of pathogenic splicing variants using RNA-seq data derived from 16 wellcharacterized and deeply-sequenced patient fibroblast samples.…”

Section: Pathogenic Splicing Events Are Characterized By Abnormalitiementioning

confidence: 99%

“…GTEx v8 fibroblast junction and BigWig data was downloaded via the recount3 R package (v1.1.2) and filtered for samples without large CNVs or chromosomal duplications and deletions (SMAFRZE = "RNASEQ") [28][29][30] . In-house RNA-seq data in the form of BAM files were converted into the BigWig format using megadepth (v1.08b) for input into dasper (v1.1.3) 31 .…”

Section: Rna-sequencing Alignment and Quality Control Of Patient Samplesmentioning

confidence: 99%

Detection of pathogenic splicing events from RNA-sequencing data using dasper

Zhang

García-Ruiz

et al. 2021

Preprint

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Although next-generation sequencing technologies have accelerated the discovery of novel gene-to-disease associations, many patients with suspected Mendelian diseases still leave the clinic without a genetic diagnosis. An estimated one third of these patients will have disorders caused by mutations impacting splicing. RNA- sequencing has been shown to be a promising diagnostic tool, however few methods have been developed to integrate RNA-sequencing data into the diagnostic pipeline. Here, we introduce dasper, an R/Bioconductor package that improves upon existing tools for detecting aberrant splicing by using machine learning to incorporate disruptions in exon-exon junction counts as well as coverage. dasper is designed for diagnostics, providing a rank-based report of how aberrant each splicing event looks, as well as including visualization functionality to facilitate interpretation. We validate dasper using 16 patient-derived fibroblast cell lines harbouring pathogenic variants known to impact splicing. We find that dasper is able to detect pathogenic splicing events with greater accuracy than existing LeafCutterMD or z-score approaches. Furthermore, by only applying a broad OMIM gene filter (without any variant-level filters), dasper is able to detect pathogenic splicing events within the top 10 most aberrant identified for each patient. Since using publicly available control data minimises costs associated with incorporating RNA-sequencing into diagnostic pipelines, we also investigate the use of 504 GTEx fibroblast samples as controls. We find that dasper leverages publicly available data effectively, ranking pathogenic splicing events in the top 25. Thus, we believe dasper can increase diagnostic yield for a pathogenic splicing variants and enable the efficient implementation of RNA-sequencing for diagnostics in clinical laboratories.

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“…There are already several tools to extract coverage information from alignment files (in BAM format): Samtools (Li et al, 2009), Bedtools (Quinlan, 2014), Sambamba (Tarasov et al, 2015) and the newer and more feature-rich Mosdepth (Pedersen and Quinlan, 2018b) and MegaDepth (Wilks et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

“…There are already several tools to extract coverage information from alignment files (in BAM format): Samtools (Li et al ., 2009), Bedtools (Quinlan, 2014), Sambamba (Tarasov et al ., 2015) and the newer and more feature-rich Mosdepth (Pedersen and Quinlan, 2018b) and MegaDepth (Wilks et al ., 2021). A common limitation of the existing tools is the inability to calculate physical coverage which is important when determining the integrity of assemblies using mate-pairs libraries.…”

Section: Introductionmentioning

confidence: 99%

BamToCov: an efficient toolkit for sequence coverage calculations

Birolo

Telatin

2021

Preprint

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Many genomics applications requires the calculation of nucleotide coverage of a reference or counting how many reads maps in a reference region.Here we present BamToCov, a suite of tools for rapid and flexible coverage calculations relying on a memory efficient algorithm and designed for flexible integration in bespoke pipelines. The tools of the suite will process sorted BAM or CRAM files, allowing to extract coverage information using different filtering approaches.BamToCov tools, unlike existing tools already available, have been developed to require a minimum amount of memory, to be easily integrated in workflows, and to allow for strand-specific coverage analyses. The unique coverage calculation algorithm makes it the ideal choice for the analysis of long reads alignments. The programs and their documentation are freely available at https://github.com/telatin/bamtocov.

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Megadepth: efficient coverage quantification for BigWigs and BAMs

Cited by 6 publications

References 12 publications

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

Detection of pathogenic splicing events from RNA-sequencing data using dasper

BamToCov: an efficient toolkit for sequence coverage calculations

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