Tag Archives: Illumina

Signal Boosting a Comprehensive Review of eDNA and Metabarcoding Studies

Everything is meta these days – metabarcoding, metagenomics, and now meta blog posts that are reviews of reviews. Much like every ecologist at least dabbles in the molecular world, so most of those predisposed to molecular ecology and population genetics … Continue reading

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Posted in bioinformatics, community ecology, DNA barcoding, metagenomics, methods, microbiology, next generation sequencing, population genetics | Tagged , , , , , , , , , , | 1 Comment

Right reads, wrong index? Concerns with data from Illumina’s HiSeq 4000

Commanding around a 70% share of a 1.3 billion USD market, Illumina is the major player in next-generation sequencing (NGS) technology. More likely than not, if you’re a molecular ecologist working with NGS data, you’ve run your samples on a … Continue reading

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Posted in genomics, next generation sequencing, RNAseq, technical, transcriptomics | Tagged , , , , | 5 Comments

The Great Migration and African-American Genomic History

Over 45 million African-Americans share a recent common history largely shaped by “The Great Migration” (1910-1970) from out of the Southern United States. And yet, the admixture history of the African-American community, and its consequences for public health are little … Continue reading

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Posted in genomics, population genetics, United States | Tagged , , , , , | Leave a comment

The 2016 Next-Generation Sequencing Field Guide Preview: Zombie Systems and New Hope

After a year of minimal activity, we finally have some significant changes in Next Gen Land. In the 2016 update of the NGS Field Guide, I will continue to give my overall interpretation about the various instruments, but with less … Continue reading

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Posted in genomics, howto, methods, RNAseq, transcriptomics | Tagged , , , | 8 Comments

New to the genome sequencing $8 menu: Nextera library preps!

Researchers are thrifty. We’re always looking for ways to make our expensive supplies and reagents go the extra mile. This shit has been going on for decades – hell, probably even centuries: I remember when I was a kid and … Continue reading

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Posted in genomics, methods, next generation sequencing | Tagged , , , , | 7 Comments

Phylogeny-aware comparisons of microbial communities – EdgePCA and Squash Clustering

I’m jumping on the bandwagon with a blog post about this new PLoS ONE paper (taking the lead from the man in charge in my lab) because the algorithms are just so exciting: Matsen FA IV, Evans SN. (2013) Edge Principal … Continue reading

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Posted in bioinformatics, genomics, next generation sequencing, software | Tagged , , , , , , , | 1 Comment

Dramatically reducing sequencing error via Duplex Tag sequencing

An exciting new study was published in PNAS last month, an open access paper entitled “Detection of ultra-rare mutations by next-generation sequencing”. This new method has the potential to open up a new frontier in Next-gen sequencing bioinformatics, since it allows … Continue reading

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Posted in methods, next generation sequencing | Tagged , , , , | 5 Comments