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Out of curiosity, what genome assembler are you using for your project? (I'm having to build a genome assembly pipeline with a reference assembly as well for a
by noname123 11y ago
Out of curiosity, what genome assembler are you using for your project? (I'm having to build a genome assembly pipeline with a reference assembly as well for a bioinformatics class I'm auditing at a local college, not a professional in this field either). The papers I am reading and trying to replicate uses SMALT.
- rfc 11y agoAssuming you're referring to the alignment side of things. We use a variation the Bowtie2 algorithm that allows us to align multiple genomes at once to the same reference genome.
- noname123 11y agoThanks for your reply, rfc. In my Bioinformatics class, we went through Bowtie algorithm funny enough last week (the vague details I still remember are the funny way it compresses fragments as rotations and then goes onto transform the rotations). Gl on your project.