After a few quite weeks on the news from Oxford Nanopore front, this week had a flurry of activities on Oxford Nanopore. Just like before, NIck Loman was behind person behind all interesting updates on @nanopore. If you missed all the action. Here is the summary of recent nanopore activities.
First, Nick Loman and Aaron Quinlan, posted a preprint on biorXiv,
Poretools: a toolkit for analyzing nanopore sequence data, by Loman and Quinlan
Poretools, as the name reveals it, is SAMtools and bedtools like computational toolkit that will let you do the most basic things with sequence data from Oxford Nanopore. Poretools is open source software written in Python and has a suite of command line utilities to operate on the data. For example, Oxford Nanopore sequence data is in HDF5 file format and poretools can let you easily convert into fastq or fasta format. Poretools also let you explore and visualize the raw data. For example, one can easily get read length distribution and the so called squiggle plot visualizing the raw signal from nanopore.
Nick Loman tweeted that Poretools is a Twitter based collaboration. Both were independently working on a tool from nanopore sequencing data and after find out they merged their work.
Here are some answers to frequently asked questions on Nanopore sequencing via Nick Loman’s illustrated tweets :)
I have multiple minIONs. How do I scale up my experiment and use all the minIONs at the same time?
What is the latest on Nanopore?
Updated nanopore chemistry and flowcells now shipping.
— Clive G. Brown (@Clive_G_Brown) July 9, 2014
How is the data quality on the new nanopore chemistry?
What is the two-directional read?
How good is the nanopore data? Can I call SNP with nanopore data?
Is the good data cherry picked? Is it the best data, or average data
Ok. Show me the data?
— Nick Loman (@pathogenomenick) July 25, 2014