This release includes the following modules:
| Pipeline | Category | Status/Changes |
|---|---|---|
| Short-Read Illumina, Paired-End | Alignment | New pipeline added |
| Long-Read PacBio HiFi | Alignment | New pipeline added |
| Long-Read Oxford Nanopore | Alignment | New pipeline added |
| Short-Read Aligned, Paired-End (BAM) | Quality Control | New pipeline added |
| Long-Read Aligned (BAM) | Quality Control | New pipeline added |
| Short-Read Unaligned (FASTQ) | Quality Control | New pipeline added |
| Software | Version | Category | Command | Source |
|---|---|---|---|---|
| BWA-MEM | 0.7.17 | Aligner | - | Sentieon 202308.01 |
| pbmm2 | 1.13.0 | Aligner | - | - |
| minimap2 | 2.26 | Aligner | - | Sentieon 202308.01 |
| Picard | 3.0.0 | Utilities | - | - |
| Picard | 2.9.0 | Utilities | LocusCollector + Dedup [MarkDuplicates] | Sentieon 202308.01 |
| GATK | 4.4.0.0 | Utilities | - | - |
| GATK | 3.8 | Utilities | Realigner [RealignerTargetCreator + IndelRealigner] | Sentieon 202308.01 |
| GATK | 4.1 | Utilities | QualCal [BaseRecalibrator], ReadWriter [ApplyBQSR] | Sentieon 202308.01 |
| methylink | 0.6.0 | Utilities | - | - |
| Samtools | 1.17 | Utilities | - | - |
| Bcftools | 1.17 | Utilities | - | - |
| fastp | 0.23.2 | Utilities | - | - |
| FastQC | v0.12.0 | Quality control | - | - |
| NanoPlot | 1.42.0 | Quality control | - | - |
Command: the specific subcommand or driver invoked, when applicable; bracketed names indicate the name of the equivalent algorithm. Source: source for the software, when it’s not the original release.