Archive For The “bioinformatics” Category

Assembling reads with velvet

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Velvet is a hash-based deBrujin assembler. I occasionally use it to build contigs from short read RNAseq data, although it can be used for long reads, metagenomics, etc. To install, just download, extract and make. There are two parts to the program: 1. velveth – prepare the sequences 2. velvetg – build the graph and…

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GMAP for long read RNA

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GMAP is an old (circa 2006) software for long read alignment. Its use case is for mapping RNA reads back to a genome. It has found new life in the world of long read RNAseq such as from Pacbio reads. Perhaps because of its age and architecture, it has some quirks and dependencies that seem…

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Using liftover

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The LiftOver tool is essentially a way for you to take a location or set of locations in one build of a genome and map it to a different build or genome. For instance, say you have a locus chr17:1000000-1000100 in human genome build hg17 and you want to know where it resides in the…

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