Table 1 Major steps of the three pipelines HybPiper, SECAPR, and Captus (differences highlighted in bold)
From: Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
| Â | HybPiper | SECAPR | Captus |
|---|---|---|---|
Input | Target Capture (short reads) | Target Capture (short reads) | Target Capture, WGS, RNASeq, Genome Skimming (short reads) |
Quality control | No | Yes | Yes |
Input target reference | protein or DNA | only DNA | protein or DNA |
Assembly | De-novo (SPAdes) Separate reads using best locus assembled with SPAdes | De-novo (SPAdes, ABySS) All reads assembled using SPAdes | De-novo (MEGAHIT) All reads assembled using MEGAHIT |
Exon/Intron recovery | Exonerate | BLASTn | Scipio |
Paralogs Filter | Yes | Yes | Yes |
Alignment | No | Yes | Yes |