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Dependencies
devantet edited this page Jul 24, 2018
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3 revisions
| Dependency | Version | Handlers |
|---|---|---|
| BBMap | v38.06 | Adapter Trimmer |
| Bedops | v2.4.35 | Coverage Summary |
| Bedtools | v2.27.1 | Coverage Summary |
| BLASTX | v2.7.1 | Read Mapping |
| Bowtie2 | v2.3.4.1. | Read Mapping |
| BWA | v0.7.17 | Read Mapping |
| CutAdapt | v1.16 | Adapter Trimmer |
| Ddocent | 2.5.5. 0. | Adapter Trimmer |
| FastQC | v0.11.7 | QC (assess quality of fastq files, trimmed fastq files, BAM) |
| FreeBayes | v1.2.0 | Variant Calling |
| GATK | v.3.8 | Variant Calling |
| LoFreq | v2.1.3.1 | Variant Calling |
| Minimap2 | v2.11 | Read Mapping |
| Platypus | v0.8.1.1 | Variant Calling |
| SAMtools | v1.9 | SAM to BAM/CRAM |
| SAMtools | v1.9 | Variant Calling |
| Scythe | v0.992 | Adapter Trimmer |
| Seqpurge | v2.0 | Adapter Trimmer |
| Skewer | v0.2.2 | Variant Calling |
| SNVer | v0.5.3 | Variant Calling |
| Stampy | v1.0.20 | Read Mapping |
| Subread | v1.6.2 | Read Mapping |
| Trim Galore | v0.5.0 | Adapter Trimmer |
| Trimmomatic | v0.38 | Adapter Trimmer |
| VarDict | v2018.07.24 | Variant Calling |
| VarScan | v2.4.3 | Variant Calling |