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Viral genomics analysis pipelines
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Changes spades default mode from rna to meta #966

Open yesimon opened 5 years ago

yesimon commented 5 years ago

The rnaSpades mode is heavily focused on mRNA transcriptome assembly and is very aggressive at splicing assemblies into short transcripts. The —meta mode would be more suitable for our DNA/RNA assembly even though it is optimized for DNA metagenomes.

One barrier is that meta spades only accepts a single paired end library and doesn’t accept unpaired reads for now. Although not too common, we should handle this by warning after Trimmomatic if a significant number of reads become orphaned.

notestaff commented 5 years ago

A branch adding metaspades is https://github.com/broadinstitute/viral-ngs/tree/is-add-metaspades