Table 1.
List of biological databases and bioinformatics tools relevant for data-warehousing, alignment, processing or analysis of sequence reads.
| Category | Bioinformatics tools | Reference |
|---|---|---|
| Read alignment | BWA | Li and Durbin, 2009 |
| Bowtie | Langmead, 2010 | |
| Annotation | Annovar (Qiagen) | Qiagen, 2018a |
| Variant Effect Predictor (Ensembl) | McLaren et al., 2016 | |
| SNPsift and SNPeffect | Cingolani et al., 2012 | |
| Variant Annotation Integrator (UCSC) | Hinrichs et al., 2016 | |
| NCBI Variant Annotation | Church et al., 2013 | |
| Sift4G | Vaser et al., 2016 | |
| WGS annotator (runnable on the Amazon Compute Cloud) | Liu et al., 2016a | |
| Visualization | NCBI Variant Viewer | National Center for Biotechnology Information, 2018 |
| UCSC Genome Browser | Kent et al., 2002 | |
| ENSEMBL Genome Browser | Stalker et al., 2004 | |
| ExAC browser | Karczewski et al., 2017 | |
| Integrative Genomics Viewer (IGV) | Thorvaldsdottir et al., 2013 | |
| Personal Genome Browser (PGB) | Juan et al., 2014 | |
| 3D Genome Browser | Wang et al., 2018b | |
| Data-warehousing | ClinVar (clinical significance) | Landrum et al., 2014 |
| dbSNP (NCBI main variant annotation database) | Sherry et al., 2001 | |
| dbNSFP (variants damage prediction using many in silico algorithms) | Liu et al., 2011 | |
| COSMIC (Catalogue of Somatic Mutations in Cancer) | Forbes et al., 2017 | |
| GWAS Catalog | Welter et al., 2014 | |
| GWAS Central | Beck et al., 2014 | |
| Cancer Atlas | Liu et al., 2018 | |
| RefSeq | Pruitt et al., 2005 | |
| PANTHER | Thomas et al., 2003 | |
| TCGA (The Cancer Genome Atlas) | Weinstein et al., 2013 | |
| ICGC (International Cancer Genome Consortium | Zhang et al., 2011 | |
| Analytics | Genome Analysis Toolkit (GATK) | DePristo et al., 2011 |
| MuTect | Cibulskis et al., 2013 | |
| OTG-snpcaller | Zhu et al., 2014 | |
| ASEQ | Romanel et al., 2015 | |
| Halvade-RNA | Decap et al., 2017 | |
| GT-WGS | Wang et al., 2018a | |
| EXCAVATOR2 | D’Aurizio et al., 2016 | |
| KaryoScan | Maxwell et al., 2017 | |
| AI-based analytics | Exomiser | Smedley et al., 2015 |
| DeepVariant | Knight, 2017 | |
| Deep Genomics | Knight, 2017 | |
| Qiagen (Ingenuity Variant Analysis and Ingenuity Pathway Analysis) | QIAGEN, 2018b | |
| Golden Helix (VarSeq, VSCkinical) | Golden Helix, 2017 | |
| Advaita (iVariant/iPatway/iBio Guides) | ADVAITA, 2018 | |
| Lifemap Sciences | TGexTM, 2018 |