Figure 3
From: Optimizing de novo assembly of short-read RNA-seq data for phylogenomics
Overall comparison among assembly strategies. (A) Number of transcripts in each category; and (B) percent reference coverage, redundancy and chimera rate among assembly strategies. Cap3: redundancy reduction using cap3; blast: trans chimera cleanup using blastx against model protein database; Oases MK filter: filter loci from Oases single k-mer assemblies by number of transcripts per locus at k = 21, 31, 41 and 51, with k = 61 not subject to filtering by number of transcripts per locus, before combining them. Oases MN: Oases-M merging single k-mer assemblies of 21, 31, 41, 51 and 61; MW: Oases-M merging single k-mer assemblies of 19–71, with increment of 2; SOAPdenovo-Trans contigs: combining contigs from SOAPdenovo-Trans single k-mer assemblies of 21, 31, 41, 51 and 61; Trans-ABySS MK: Trans-ABySS merging single k-mer assemblies of 21, 31, 41, 51 and 61; Trinity pickH: only keeping the transcript with the highest read coverage for each subcomponent; Trinity removeL: when there are two or more transcripts per subcomponent, remove the one with the lowest read coverage.