We blog about genomics. We also make a platform for open-source analysis of next generation data in the cloud. Hello.

Better sequences (and fewer homopolymer errors) for Ion Torrent

The short read files that Ion Torrent’s sequencing machines give us still contain many homopolymer errors: errors in the number of bases called when a single nucleotide occurs more than once in sequence. This makes alignment harder and drowns real indels in a sea of noise. These homopolymer errors arise …

Written by Nate

A mystery muscle lincRNA

We know that our whole genome is distributed to (almost) every cell of our bodies. This fact can be used both to surprise introductory biology students and to usefully refine a fundamental scientific question. Instead of merely asking how it comes to be that different parts of our bodies have …

Written by Nate

RNA-Seq Interactive Literature Review

RNA-Seq is fast becoming the top method for examining the transcriptional activity of genomes. In the five years since the first publications described the technology, RNA-Seq has enabled the discovery of new transcripts in well-studied genomes, challenged our views of imprinting, offered insights into the biology of cancer, and transformed new …

Written by Kate Blair

Short read alignment: seeding

In my last post I explained some of the basics of short read alignment algorithms. Go read it if you like; if not, recall that: Many modern alignment algorithms rely on what is called seeding and extending. “Seeding” is finding exact matches of part of the read with part of the …

Written by Nate

Short read alignment: an introduction

Biologists today often find themselves with lots of–say, 10^6–short sequences of DNA from a sample, and their ability to do scientifically useful things with those sequences depends on their ability to align those sequences to a reference sequence. Many of the hard and important projects in genomics either are alignment …

Written by Nate

Seven Bridges Platform wins BioIT World Best of Show

We’ve been working pretty hard over the past few years to build a tool for next generation sequence data analysis that we love. So we were very pleased to see Seven Bridges Platform win Best of Show in the Informatics Data & Tools division at BioIT World 2013. Seven Bridges …

Written by Kate Blair

Unicorn genome sequence announced

A landmark genome announcement was made by the Equid Sequencing Consortium today. Scientists hope that the new data will explain origins of the horn and help identify key genes that drive horn development. A high-quality draft of unicorn genome was published today and will be submitted to GenBank later this spring.

Written by brandi

Visualizing exome coverage depth

The coverage of a base pair in a sequencing run is the number of times that it was sequenced. We usually estimate coverage in an intuitive way: by comparing the total amount of measurement to the total amount of stuff to be measured. Dividing the total length of the reads …

Written by Nate

Cloud-based NGS analysis makes it to Nature

You know a technology has made it when it shows up in a print page of Nature. So we were pleased to see that Vol. 495, Issue 293, released today, includes a piece on the rise of cloud-based next-generation sequence (NGS) analysis. The past year of conferences has given us …

Written by Kate Blair

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