Bazam A rapid method for read extraction and realignment of high throughput sequencing data, bioRxiv, 2018-10-04

AbstractBackgroundAs costs of high throughput sequencing have fallen, we are seeing vast quantities of short read genomic data being generated. Often, the data is exchanged and stored as aligned reads, which provides high compression and convenient access for many analyses. However, aligned data becomes outdated as new reference genomes and alignment methods become available. Moreover, some applications cannot utilise pre-aligned reads at all, necessitating conversion back to raw format (FASTQ) before they can be used. In both cases, the process of extraction and realignment is expensive and time consuming.FindingsWe describe Bazam, a tool that efficiently extracts the original paired FASTQ from reads stored in aligned form (BAM or CRAM format). Bazam extracts reads in a format that directly allows realignment with popular aligners with high concurrency. Through eliminating steps and increasing the accessible concurrency, Bazam facilitates up to a 90% reduction in the time required for realignment compared to standard methods. Bazam can support selective extraction of read pairs from focused genomic regions, further increasing efficiency for targeted analyses. Bazam is additionally suitable as a base for other applications that require efficient paired read information, such as quality control, structural variant calling and alignment comparison.ConclusionsBazam offers significant improvements for users needing to realign genomic data.

biorxiv bioinformatics 200-500-users 2018

Collective intercellular communication through ultra-fast hydrodynamic trigger waves, bioRxiv, 2018-09-27

The biophysical relationships between sensors and actuators have been fundamental to the development of complex life forms; abundant flows are generated and persist in aquatic environments by swimming organisms, while responding promptly to external stimuli is key to survival. Here, akin to a chain reaction, we present the discovery of hydrodynamic trigger waves in cellular communities of the protist Spirostomum ambiguum, propagating hundreds of times faster than the swimming speed. Coiling its cytoskeleton, Spirostomum can contract its long body by 50% within milliseconds, with accelerations reaching 14g-forces. Surprisingly, a single cellular contraction (transmitter) is shown to generate long-ranged vortex flows at intermedi- ate Reynolds numbers, which can trigger neighbouring cells, in turn. To measure the sensitivity to hydrodynamic signals (receiver), we further present a high-throughput suction-flow device to probe mechanosensitive ion channel gating by back-calculating the microscopic forces on the cell mem- brane. These ultra-fast hydrodynamic trigger waves are analysed and modelled quantitatively in a universal framework of antenna and percolation theory. A phase transition is revealed, requiring a critical colony density to sustain collective communication. Our results suggest that this signalling could help organise cohabiting communities over large distances, influencing long-term behaviour through gene expression, comparable to quorum sensing. More immediately, as contractions release toxins, synchronised discharges could also facilitate the repulsion of large predators, or conversely immobilise large prey. We postulate that beyond protists numerous other freshwater and marine organisms could coordinate with variations of hydrodynamic trigger waves.

biorxiv biophysics 200-500-users 2018

 

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