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Sharing benchmarking results for short read assembler on paired end Illumina data
We recently wrapped up some work on benchmarking the more recent genome assemblers on a range of genomes with Illumina paired end sequence data. We compared a few of the most common metrics, one metric we included was the number of correct genes in an assembly. The overall best assembler for this metric was the JGI isolate assembly pipeline which used BBMap preprocessing steps and spades as the assembler.
The outline of this is here:
A github repo for a docker image with this assembler is here:
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Many organizations study rare diseases, but few have a mission as impactful as Rady Children’s Institute for Genomic Medicine (RCIGM). “We are all about changing outcomes for children,” explained Dr. Stephen Kingsmore, President and CEO of the group. The institute’s initial goal was to provide rapid diagnoses for critically ill children and shorten their diagnostic odyssey, a term used to describe the long and arduous process it takes patients to obtain an accurate...12-16-2024, 07:57 AM -
Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.
Long-Read Sequencing
Long-read sequencing has seen remarkable advancements,...12-02-2024, 01:49 PM
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