Program Dictionary
Mapping
Whole genome NGS
| Program | Description |
|---|---|
| BWA mem | Standard program for mapping Illumina whole genome NGS |
| minimap2 | Mapping for noisy long reads such as minION or PacBio |
RNA-seq
| Program | Description |
|---|---|
| STAR | RNA-seq mapping for eukaryotic organisms |
| TopHat | RNA-seq mapping eukaryotic and prokaryotic data |
| BWA mem | RNA-seq mapping for prokaryotic. Only useful if there is no splicing |
| DESeq2 | Differential expression analysis for RNAseq |
| Kallisto | Speedy RNA-seq quantification |
BAM manipulation
| Program | Description |
|---|---|
| SAMtools | Format conversion, region extraction, sorting, pileup |
Variant calling
| Program | Description |
|---|---|
| BCFtools | Variant calling, annotation, extraction, format conversion |
| LoFreq | Rare variant calling |
| Delly | Read alignment based SV calling (DUP, DEL, INS, INV, TRA) |
| CNVNator | Read depth based CNV calling |
| FREEC | Read depth based CNV calling |
Imputation
| Program | Description |
|---|---|
| Beagle | vcf Phasing and Imputation |