@assemblathon profile picture
The Assemblathon @assemblathon

I tweet about genome assembly and related topics. If something happens in the world of genome assembly and I don’t tweet about it…then it didn’t really happen.

Joined November 2010
  • Tweets 5,011
  • Following 128
  • Followers 3,886
60 Photos and videos
Validation of reference-assisted assembly using existing and novel Heliothine genomes - ScienceDirect buff.ly/3p2aZLk
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CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes biorxiv.org/content/10.1101/…

CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes

Using long reads provides higher contiguity and better genome assemblies. However, producing such high quality sequences from raw reads requires to chain a growing set of tools, and determining the...

biorxiv.org
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Benchmarking and Assessment of Eight De Novo Genome Assemblers on Viral Next-Generation Sequencing Data, Including the SARS-CoV-2 | OMICS: A Journal of Integrative Biology liebertpub.com/doi/10.1089/o…

Benchmarking and Assessment of Eight De Novo Genome Assemblers on Viral Next-Generation Sequencing...

Viral genomics has become crucial in clinical diagnostics and ecology, not to mention to stem the COVID-19 pandemic. Whole-genome sequencing (WGS) is pivotal in...

journals.sagepub.com
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Learning to Untangle Genome Assembly with Graph Convolutional Networks arxiv.org/abs/2206.00668v1

Learning to Untangle Genome Assembly with Graph Convolutional Networks

A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous...

arxiv.org
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Learning to Untangle Genome Assembly with Graph Convolutional Networks arxiv.org/abs/2206.00668v1

Learning to Untangle Genome Assembly with Graph Convolutional Networks

A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous...

arxiv.org
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The Assemblathon retweeted
Nicolás Nahuel Moreyra@NicoMoreyra
24 May 2022
Does anyone have recommendations on programs for genome alignment and synteny analysis? #pacbio #genomealignment #synteny #assembly #genomeassembly @assemblathon
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HGGA: hierarchical guided genome assembler - BMC Bioinformatics bmcbioinformatics.biomedcent…

HGGA: hierarchical guided genome assembler

BMC Bioinformatics - De novo genome assembly typically produces a set of contigs instead of the complete genome. Thus additional data such as genetic linkage maps, optical maps, or Hi-C data is...

link.springer.com
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Benchmarking of long-read sequencing, assemblers and polishers for yeast genome academic.oup.com/bib/advance…

Benchmarking of long-read sequencing, assemblers and polishers for yeast genome

AbstractBackground. The long reads of the third-generation sequencing significantly benefit the quality of the de novo genome assembly. However, its relati

academic.oup.com
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slag: A program for seeded local assembly of genes in complex genomes onlinelibrary.wiley.com/doi/…

slag: A program for seeded local assembly of genes in complex genomes

Although finished genomes have become more common, there is still a need for assemblies of individual genes or chromosomal regions when only unassembled reads are available. slag (Seeded Local...

onlinelibrary.wiley.com
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Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation - Nature Methods nature.com/articles/s41592-0…
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NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology peerj.com/articles/13056

NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of...

Background Next Generation Sequencing (NGS) techniques dominate today’s landscape of genetics and genomics research. Though Illumina still dominates worldwide sequencing, Oxford Nanopore is one of...

peerj.com
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The Assemblathon retweeted
Michael Schatz@mike_schatz
31 Mar 2022
So proud and excited for our #T2T work on "A complete reference genome improves analysis of human genetic variation"! Im enormously grateful to the whole team for their tireless work and support @JHU_BDPs @JHUCompSci @HopkinsCMDB science.org/doi/10.1126/scie…

A complete reference genome improves analysis of human genetic variation

Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands of structural errors, and unlocks the most complex regions of...

science.org
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The Assemblathon retweeted
Keith Robison@OmicsOmicsBlog
31 Mar 2022
The End of the Beginning of Human Genome Sequencing? Quick thoughts on today's #T2T publishing barrage omicsomics.blogspot.com/2022…

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The Assemblathon retweeted
Alyssa Phillips@Plant_Phillips
9 Mar 2022
Happy to share this happy accident and collaboration we've been working on for the last two years! In summary: We accidentally assembled a Poa pratensis reference genome. biorxiv.org/content/10.1101/…

A happy accident: a novel turfgrass reference genome

Poa pratensis , commonly known as Kentucky bluegrass, is a popular cool-season grass species used as turf in lawns and recreation areas globally. Despite its substantial economic value, a reference...

biorxiv.org
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Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads - Nature Biotechnology nature.com/articles/s41587-0…

Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads

Nature Biotechnology - A multiplex de Bruijn graph algorithm allows high-accuracy genome assembly from long, high-fidelity reads.

nature.com
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High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads biorxiv.org/content/10.1101/…

High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

Arabidopsis thaliana is an important and long-established model species for plant molecular biology, genetics, epigenetics, and genomics. However, the latest version of reference genome still...

biorxiv.org
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A simple guide to de novo transcriptome assembly and annotation academic.oup.com/bib/advance…

A simple guide to de novo transcriptome assembly and annotation

Abstract. A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily attainable proxy catalog of protein-coding genes when genome as

academic.oup.com
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De Novo Assembly of Linked Reads Using Supernova 2.0 link.springer.com/protocol/1…
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Graph theoretical Strategies in De Novo Assembling ieeexplore.ieee.org/abstract…
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ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs - Abstract - Europe PMC buff.ly/3HIIg5A
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