Table 1 Tracy feature comparison
From: Tracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files
Core functions | Tracy | novoSNP | GeneScreen |
|---|---|---|---|
Basecalling | ✓ | ✓ | ✓ |
FASTA alignment | ✓ | ✓ | ✓ |
Wildtype chromatogram alignment | ✓ | ✓ | ✓ |
Large genome alignment | ✓ | ✗ | ✗ |
Variants | |||
InDel decomposition | ✓ | ✓ | ✓ |
Variant calling | ✓ | ✓ | ✓ |
Variant genotyping | ✓ | ✓ | ✓ |
Variant annotation | ✓ | ✓ | ✓ |
Assembly | |||
Trace assembly | ✓ | ✓ | ✗ |
Patching reference sequences | ✓ | ✓ | ✗ |
File support | |||
Trace formats (abi, ab1, scf) | ✓ | ✓ | ✓ |
BCF/VCF support | ✓ | ✗ | ✗ |
GUI | |||
Windows Desktop Application | ✗ | ✓ | ✓ |
Web applications | ✓ | ✗ | ✗ |
Command-line application | ✓ | ✓ | ✗ |
Distribution | |||
Free and open-source for commercial and private use | ✓ | ✗ | ✗ |
Source code distribution package | ✓ | ✓ | ✗ |
Binary executable | ✓ | ✓ | ✓ |
Availability of Docker/Singularity container | ✓ | ✗ | ✗ |
Bioconda package | ✓ | ✗ | ✗ |