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Dependencies
Paul Hoffman edited this page Nov 7, 2016
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| Dependency | Version | Handlers |
|---|---|---|
| Bioawk | v1.0 | Not-yet implemented |
| Seqqs | Commit 3d05375
|
Quality_Trimming |
| Sickle | v1.33 | Quality_Trimming |
| Scythe | Commit 20d3cff
|
Adapter_Trimming |
| SAMTools | 1.3.X | SAM_Processing (SAMtools and Picard) |
| R | 3.1.1 | Quality_Trimming, Coverage_Mapping |
| FastQC | 0.11.2 | Quality_Assessment |
| Portable Batch System (PBS) | 4.2.9 | All Handlers |
| GNU Parallel | 20141122 | Quality_Assessment, Read_Depths, Adapter_Trimming, Quality_Trimming, SAM_Processing (SAMtools), Coverage_Mapping |
| Burrows-Wheeler Aligner (BWA) | 0.7.12 | Read_Mapping |
| Picard | 2.1.1 | SAM_Processing (Picard) |
| Java | 1.8 | SAM_Processing (Picard), Indel_Realignment |
| Bedtools | 2.23.0 | Coverage_Mapping |
| GATK | 3.3.0 | Indel_Realignment |
Note: later versions of SAMtools (1.3 was tested) will not work with sequence handling.
Next: FAQ and Troubleshooting
Or if you want to jump straight to running the program, step one is Quality_Assessment.
- Getting Started
- Recommended Workflow
- Configuration
- Dependencies
- sample_list_generator.sh
- Slurm specific options
- Common Problems and Errors