ARCS: Assembly Roundup by Chromium Scaffolding

Yeo, Sarah; Coombe, Lauren; Chu, Justin; Rm, Warren; Birol, İnanç

doi:10.1101/100750

Cited by 12 publications

(8 citation statements)

References 17 publications

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“…We used tigmint (Jackman et al 2018) with settings as=100, depth_treshold=65, minsize=2000, number of mismatches=5 to break contigs at suspected misassemblies and low-quality regions. Next, arcs (Yeo et al 2017) was used to scaffold the contigs using settings c = 5, e=30000 and r=0.05, followed by links v1.8.5 (also from the arcs pipeline)…”

Section: Misassembly Detection and Scaffolding With Linked-read Datamentioning

confidence: 99%

Genomics of an avian neo-sex chromosome reveals the evolutionary dynamics of recombination suppression and sex-linked genes

Sigeman

Strandh

Proux‐Wéra

et al. 2020

Preprint

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How the avian sex chromosomes first evolved from autosomes remains elusive as 100 million years (Myr) of divergence and degeneration obscure their evolutionary history. Sylvioidea songbirds is an emerging model for understanding avian sex chromosome evolution because a unique chromosome fusion event ∼24 Myr ago has formed enlarged “neo-sex chromosomes” consisting of an added (new) and an ancestral (old) part. Here, we report the female genome (ZW) of one Sylvioidea species, the great reed warbler (Acrocephalus arundinaceus). We confirm that the added region has been translocated to both Z and W, and show that the added-W part has been heavily reorganised within itself and with the ancestral-W. Next, we show that recombination between Z and W continued after the fusion event, and that recombination suppression took ∼10 Myr to be completed and arose locally and non-linearly along the sex chromosomes. This pattern is inconsistent with that of large inversions and instead suggests gradual and mosaic recombination suppression. We find that the added-W mirrors the ancestral-W in terms of repeat accumulation, loss of genetic variation, and gene degeneration. Lastly, we show that genes being maintained on W are slowly evolving and dosage sensitive, and that highly conserved genes across broad taxonomic groups, regardless of sex-linkage, evolve slower on both Z and W. This study reveals complex expansion of recombination suppression along avian sex chromosomes, and that the evolutionary trajectory of sex-linked genes is highly predictable and governed partly by sex-linkage per se, partly by their functional properties.

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Section: Misassembly Detection and Scaffolding With Linked-read Datamentioning

confidence: 99%

Genomics of an avian neo-sex chromosome reveals the evolutionary dynamics of recombination suppression and sex-linked genes

Sigeman

Strandh

Proux‐Wéra

et al. 2020

Preprint

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“…Second, 10X reads were realigned to the genome using Long Ranger v2.1.1 and the alignment file was processed with Pilon v1.22 (28). Third, the same 10X reads were aligned to the genome with BWA-MEM v0.7.12-r1039 (29) and the alignment file was processed with ARCS v1.0.1 (30) to scaffold the genome. Both tools were run with default parameters.…”

Section: Assembly Results and Quality Assessmentmentioning

confidence: 99%

Genome sequence of the euryhaline Javafish medaka, Oryzias javanicus: a small aquarium fish model for studies on adaptation to salinity

Takehana

Zahm

Cabau

et al. 2019

Preprint

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41 Background: The genus Oryzias is constituted of 35 medaka-fish species each exhibiting various 42 ecological, morphological and physiological peculiarities and adaptations. Beyond of being a 43 comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex 44 determination, behaviour, morphology or adaptation through comparative genomic approaches, 45 all medaka species share many advantages of experimental model organisms including small size 46 and short generation time, transparent embryos and genome editing tools for reverse and 47

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“…To scaffold our assembly with the Chromium data, we developed ARCS (Yeo et al 2017). Briefly, we aligned the Chromium linked reads to the input BioNano scaffolds with BWA-MEM and recorded the barcodes of the reads that aligned to each scaffold.…”

Section: Scaffolding With Chromium Datamentioning

confidence: 99%

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

et al. 2017

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The assembly of DNA sequences de novo is fundamental to genomics research. It is the first of many steps toward elucidating and characterizing whole genomes. Downstream applications, including analysis of genomic variation between species, between or within individuals critically depend on robustly assembled sequences. In the span of a single decade, the sequence throughput of leading DNA sequencing instruments has increased drastically, and coupled with established and planned large-scale, personalized medicine initiatives to sequence genomes in the thousands and even millions, the development of efficient, scalable and accurate bioinformatics tools for producing high-quality reference draft genomes is timely. With ABySS 1.0, we originally showed that assembling the human genome using short 50-bp sequencing reads was possible by aggregating the half terabyte of compute memory needed over several computers using a standardized message-passing system (MPI). We present here its redesign, which departs from MPI and instead implements algorithms that employ a Bloom filter, a probabilistic data structure, to represent a de Bruijn graph and reduce memory requirements.

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ARCS: Assembly Roundup by Chromium Scaffolding

Cited by 12 publications

References 17 publications

Genomics of an avian neo-sex chromosome reveals the evolutionary dynamics of recombination suppression and sex-linked genes

Genomics of an avian neo-sex chromosome reveals the evolutionary dynamics of recombination suppression and sex-linked genes

Genome sequence of the euryhaline Javafish medaka, Oryzias javanicus: a small aquarium fish model for studies on adaptation to salinity

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

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