This release includes the following modules:
| Pipeline | Category | Status/Changes |
|---|---|---|
| Short-Read Illumina, Paired-End | Alignment | No change since 0.1.0 |
| Long-Read PacBio HiFi | Alignment | No change since 0.0.1 |
| Long-Read Oxford Nanopore | Alignment | No change since 0.0.1 |
| Short-Read RNA-seq, Paired-End | Alignment, Quality Control, Analysis | + GENCODE release updated (v45 -> v47) + Added tissues classifier + Added VerifyBamID |
| Long-Read RNA-seq, PacBio Kinnex | Alignment, Quality Control, Analysis | New pipeline added |
| Short-Read Aligned, Paired-End (BAM) | Quality Control | No change since 0.1.0 |
| Long-Read Aligned (BAM) | Quality Control | No change since 0.1.0 |
| Short-Read Unaligned (FASTQ) | Quality Control | No change since 0.1.0 |
| Long-Read Unaligned (FASTQ, uBAM) | Quality Control | + NanoPlot version updated (1.42.0 -> 1.44.1) |
| Sample Identity Check | Quality Control | New pipeline added |
| Software | Category | Version | Commands | Source |
|---|---|---|---|---|
| BWA | Aligner | 0.7.17 | - | Sentieon 202308.01 |
| pbmm2 | Aligner | 1.13.0 | - | - |
| minimap2 | Aligner | 2.26 | - | Sentieon 202308.01 |
| STAR | Aligner | 2.7.10b | - | Sentieon 202308.01 |
| Picard | Utilities | 3.0.0 | - | - |
| Picard | Utilities | 2.9.0 | MarkDuplicates | Sentieon 202308.01 |
| GATK | Utilities | 4.4.0.0 | - | - |
| GATK | Utilities | 3.8 | RealignerTargetCreator, IndelRealigner | Sentieon 202308.01 |
| GATK | Utilities | 4.1 | BaseRecalibrator, ApplyBQSR | Sentieon 202308.01 |
| methylink | Utilities | 0.6.0 | - | - |
| Samtools | Utilities | 1.17 | - | - |
| Bcftools | Utilities | 1.17 | - | - |
| fastp | Utilities | 0.23.2 | - | - |
| pbtk | Utilities | 3.4.0 | - | - |
| FastQC | Quality control | v0.12.0 | - | - |
| NanoPlot | Quality control | 1.44.1 | - | - |
| VerifyBamID2 | Quality control | 2.0.1 | - | - |
| Kraken2 | Quality control | v2.1.3 | - | - |
| mosdepth | Quality control | v0.3.9 | - | - |
| Somalier | Quality control | v0.2.19 | - | - |
| RSEM | Analysis | v1.3.3 | - | - |
| RNA-SeQC | Analysis, Quality control | 2.4.2 | - | - |
| IsoSeq | Analysis, Quality control | 4.2.0 | - | - |
| Pigeon | Analysis, Quality control | 1.3.0 | - | - |
Commands: subset of commands used from the corresponding version; Source: source for the software, when it’s not the original release