Table 2.
Popular short read processing pipelines. Full circles stand for ‘Applies’, half circles for ‘Partly applies’, and empty circles for ‘Does not apply’ for the respective category of the pipeline.
| Read cleaning | Sequence engineering | Intron recovery | MSA generation | Allele phasing | SNP extraction | Ease of installation | |
|---|---|---|---|---|---|---|---|
| aTRAM (Allen et al., 2017) | ○ | ● | ● | ○ | ○ | ○ |
|
| HYBPIPER (Johnson et al., 2016) | ○ | ● | ● | ○ | ○ | ○ |
|
| PHYLUCE (Faircloth, 2016) |
|
○ | ○ | ● | ● |
|
● |
| SECAPR (Andermann et al., 2018) | ● |
|
|
● | ● |
|
● |