Tag Archives: bioinformatics

In the pipeline – Part 1: ‘Plan, plan, and plan some more’

Posted on 10 Mar, 2021 by Rishi De-Kayne

So you’ve decided it’s time to finally get around to starting that sequencing project. But before you aimlessly leap into it and generate terabytes of sequencing data, just STOP. It’s far too tempting to rush into sequencing projects for a … Continue reading →

Posted in bioinformatics, evolution, genomics, howto, methods, population genetics, Uncategorized | Tagged assembly, bioinformatics, genetics, genomics, In the pipeline, population genetics, Sequencing | Leave a comment

A Highlight of Molecular Ecology outside of Academia

Posted on 21 Dec, 2018 by Katharine Coykendall

I’ve recently made a career change. Actually, I’m not even sure whether to call it that, or the next step of a natural, if meandering progression of a scientist not on the academic career path. Even though I see more and … Continue reading →

Posted in career, conservation, ecology, funding, pedigree, population genetics, quantitative genetics, Uncategorized | Tagged academia, alternative careers, bioinformatics, conservation, fisheries, SNPs | Leave a comment

Metabarcoding for every body, every habitat, every time

Posted on 19 Jul, 2018 by Laetitia Wilkins

The immediate reason why I wanted to write about Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles is its usefulness for the scientific community and the effort of the authors to make their study reproducible. … Continue reading →

Posted in bioinformatics, community, community ecology, DNA barcoding, fieldwork, metagenomics, next generation sequencing, phylogenetics, R | Tagged biodiversity, bioinformatics, ecology, metabarcoding, methods, microbiome, phylogenetics | 1 Comment

What is DAS? A new tool to recover genomes from metagenomes

Posted on 8 Jun, 2018 by Kelle Freel

There are a lot of data out there, and if you haven’t already noticed the ‘omics train has steadily stayed its path through the fruitful (but challenging) world of metagenomics. Metagenomics offers the chance to unravel complex microbial communities without … Continue reading →

Posted in bioinformatics, community ecology, genomics, metagenomics, methods, microbiology, next generation sequencing | Tagged bioinformatics, Environmental microbiology, Genome assembly algorithms, software | Leave a comment

Signal Boosting a Comprehensive Review of eDNA and Metabarcoding Studies

Posted on 10 Apr, 2018 by Katharine Coykendall

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 →

Posted in bioinformatics, community ecology, DNA barcoding, metagenomics, methods, microbiology, next generation sequencing, population genetics | Tagged barcode tags, barcoding, bioinformatics, eukaryotes, Illumina, metagenomics, methods, microbial communities, microbial community analysis, microbiome, NGS | 1 Comment

Major new microbial groups expand diversity and alter our understanding of the tree of life

Posted on 18 Mar, 2018 by Laetitia Wilkins

I still believe in revolutions. And sometimes they just happen, almost unnoticed. One such revolution happened on a boring 11th of April 2016 when Laura Hug et al. published their new tree of life in the journal of Nature Microbiology. … Continue reading →

Posted in bioinformatics, community ecology, evolution, genomics, metagenomics, microbiology, next generation sequencing, phylogenetics | Tagged assembly, bioinformatics, Evolution, genome, genomics, metagenomics, NGS, phylogenetics | 1 Comment

Easily aggregate bioinformatic sample output with one tool

Posted on 3 Jul, 2017 by Elin Videvall

Today I’m going to write about one of my favorite bioinformatic tools, MultiQC. If you’ve used it, you know why, and if you haven’t, prepare to be amazed. Many bioinformatic software produce output on a per-sample basis. That is, you … Continue reading →

Posted in bioinformatics, next generation sequencing, software | Tagged bioinformatics, multiqc, software | Leave a comment

Handling microbial contamination in NGS data

Posted on 6 Jan, 2017 by Ethan Linck

Until recently, I had given little thought to the potential for unwanted microbial contamination in high throughput sequence data. I suspect that if you’re a molecular ecologist who doesn’t primarily study microbes or work with ancient DNA, you’re in a … Continue reading →

Posted in bioinformatics, genomics, howto, next generation sequencing, technical | Tagged bioinformatics, contamination, microbes, microbial contamination | Leave a comment

Using R to mine species data

Posted on 30 Mar, 2016 by Katie Everson

Many of us generate more data than we know what to do with (speaking of which: keep an eye out for the 2016 NGS Field Guide, coming soon!), so it’s easy to forget about the piles of data already at our fingertips. Research potential is … Continue reading →

Posted in howto | Tagged bioinformatics, collections, conservation, how to, occurrence, R | 12 Comments

To find duplicated loci in vertebrate polyploids, try thinking small

Posted on 23 Mar, 2016 by Rob Denton

Big sequencing efforts have gone a long way to help understand the complexities of polyploidy. However, the bioinformatic approaches to sorting and scoring alleles in next-gen data are generally designed for easy of use in diploid species. Unlike a diploid species, where … Continue reading →

Posted in genomics, methods, next generation sequencing, Uncategorized | Tagged bioinformatics, genomes, polyploidy | 3 Comments