Table 2. MpGAP pipeline core software components.
| Software | Function | Source code | Version |
|---|---|---|---|
| SPAdes | Assembler | github.com/ablab/spades | 3.15.3 |
| Unicycler | Assembler | github.com/rrwick/Unicycler | 0.4.8 |
| Shovill | Assembler | github.com/tseemann/shovill | 1.1.0 |
| Megahit | Assembler | github.com/voutcn/megahit | 1.2.9 |
| Haslr | Assembler | github.com/vpc-ccg/haslr | 0.8a1 |
| Canu | Assembler | github.com/marbl/canu | 2.2 |
| Flye | Assembler | github.com/fenderglass/Flye | 2.9 |
| Raven | Assembler | github.com/lbcb-sci/raven | 1.6.1 |
| Shasta | Assembler | github.com/chanzuckerberg/shasta | 0.8.0 |
| Wtdbg2 | Assembler | github.com/ruanjue/wtdbg2 | 2.5 |
| Pilon | Error correction | github.com/broadinstitute/pilon | 1.24 |
| Nanopolish | Error correction | github.com/jts/nanopolish | 0.13.2 |
| Medaka | Error correction | github.com/nanoporetech/medaka | 1.4.0 |
| Gcpp | Error correction | github.com/PacificBiosciences/gcpp | 2.0.2 |
| Quast | Quality control | github.com/ablab/quast | 5.0.2 |
| MultiQC | Summary report | github.com/ewels/MultiQC | 1.11 |