Accuracy, speed and error tolerance of short DNA sequence aligners

Ziemann, Mark

doi:10.1101/053686

Cited by 8 publications

(5 citation statements)

References 22 publications

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“…For instance, during the hybridization step, it is possible for historical DNA target sequences with some mismatch to nevertheless hybridize to the template probes. Moreover, during the phyloHyRAD bioinformatic mapping step, the use of the more relaxed BWA-MEM mapping algorithm instead of the more stringent BWA-ALN allowed for the recovery of much more data than anticipated ( Ziemann 2016 ). Our strategy of distributing the probe-producing samples across the expected diversity in the phylogeny has made it possible to obtain homologous sequences for species that are phylogenetically distant.…”

Section: Resultsmentioning

confidence: 99%

HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution

Toussaint

Gauthier

Bilat

et al. 2021

Genome Biology and Evolution

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Advances in phylogenomics contribute towards resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and UCE reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae beetles, the lack of which had precluded study of macroevolutionary trends pertaining to their biogeography and wing-morphology evolution. We successfully recovered up to 2945 loci with a mean of 1788 loci across the exome of specimens of varying age. Coverage was not significantly linked to specimen age, demonstrating the wide exploitability of museum specimens. We also recovered fragmentary mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct Aplothorax nested within the genus Calosoma demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosoma (Ctenosta) burchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level datasets informative at deep evolutionary scales.

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Section: Resultsmentioning

confidence: 99%

HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution

Toussaint

Gauthier

Bilat

et al. 2021

Genome Biology and Evolution

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“…Meanwhile, the alignment tool BWA-MEM was used in ChimeraMiner, and the previous pipeline used SOAP2. BWA-MEM was considered to take less time in paired-end reads alignment than SOAP2 does [35,36,37]. Besides, the SAM format [38] can alleviate the difficulty of the following analysis and reduce time.…”

Section: Discussionmentioning

confidence: 99%

ChimeraMiner: An Improved Chimeric Read Detection Pipeline and Its Application in Single Cell Sequencing

Lü

et al. 2019

IJMS

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As the most widely-used single cell whole genome amplification (WGA) approach, multiple displacement amplification (MDA) has a superior performance, due to the high-fidelity and processivity of phi29 DNA polymerase. However, chimeric reads, generated in MDA, cause severe disruption in many single-cell studies. Herein, we constructed ChimeraMiner, an improved chimeric read detection pipeline for analyzing the sequencing data of MDA and classified the chimeric sequences. Two datasets (MDA1 and MDA2) were used for evaluating and comparing the efficiency of ChimeraMiner and previous pipeline. Under the same hardware condition, ChimeraMiner spent only 43.4% (43.8% for MDA1 and 43.0% for MDA2) processing time. Respectively, 24.4 million (6.31%) read pairs out of 773 million reads, and 17.5 million (6.62%) read pairs out of 528 million reads were accurately classified as chimeras by ChimeraMiner. In addition to finding 83.60% (17,639,371) chimeras, which were detected by previous pipelines, ChimeraMiner screened 6,736,168 novel chimeras, most of which were missed by the previous pipeline. Applying in single-cell datasets, all three types of chimera were discovered in each dataset, which introduced plenty of false positives in structural variation (SV) detection. The identification and filtration of chimeras by ChimeraMiner removed most of the false positive SVs (83.8%). ChimeraMiner revealed improved efficiency in discovering chimeric reads, and is promising to be widely used in single-cell sequencing.

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“…All metagenomic, metatranscriptome, and metaviromic reads were mapped to the pooled set of viral and non-viral contigs using bowtie2, 81 , 82 with counts and breadth of coverage calculated using samtools depth. 70 A breadth of coverage threshold of ≥75% of the contig should have a minimum depth of ≥1 read per bp was applied to metagenome and metavirome count tables; counts under this threshold was set to 0.…”

Section: Methods Detailsmentioning

confidence: 99%

Multiomic spatial analysis reveals a distinct mucosa-associated virome

et al. 2023

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The human gut virome has been increasingly explored in recent years. However, nearly all virome-sequencing efforts rely solely on fecal samples and few studies leverage multiomic approaches to investigate phage–host relationships. Here, we combine metagenomics, metaviromics, and metatranscriptomics to study virome-bacteriome interactions at the colonic mucosal-luminal interface in a cohort of three individuals with inflammatory bowel disease; non-IBD controls were not included in this study. We show that the mucosal viral population is distinct from the stool virome and houses abundant crAss-like phages that are undetectable by fecal sampling. Through viral protein prediction and metatranscriptomic analysis, we explore viral gene transcription, prophage activation, and the relationship between the presence of integrase and temperate phages in IBD subjects. We also show the impact of deep sequencing on virus recovery and offer guidelines for selecting optimal sequencing depths in future metaviromic studies. Systems biology approaches such as those presented in this report will enhance our understanding of the human virome and its interactions with our microbiome and our health.

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Accuracy, speed and error tolerance of short DNA sequence aligners

Cited by 8 publications

References 22 publications

HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution

HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution

ChimeraMiner: An Improved Chimeric Read Detection Pipeline and Its Application in Single Cell Sequencing

Multiomic spatial analysis reveals a distinct mucosa-associated virome

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