Table 5.
Selected software solutions for data handling, error detections, bioinformatic analyses and publications a.
| Category | Tools |
|---|---|
| Citation Managers | Zotero, EndNote, Mendeley, Paperpile, Citavi, JabRef, ReadCube, Papers, RefWorks, Cite This For Me |
| Data Cleaning | OpenRefine, Talend Data Quality, KNIME |
| Data Repositories | NCBI Sequence Read Archive (SRA), European Nucleotide Archive (ENA), DNA Data Bank of Japan (DDBJ), Sequence Read Archive in the Cloud (SRA in the Cloud), GenBank |
| Genome Visualization | IGV, MAKER, PANTHER, HPIDB, MITOS |
| Annotation Tools | GenSAS, Apollo, PubTator |
| Annotation Databases | BioMart, Ensembl, Ensembl Genomes, NCBI Gene, GeneCards, UniProt, RefSeq, PDB, InterPro, dbSNP, COSMIC |
| Sequence Alignment and Annotation | BLAST, MAFFT, Prokka, ANNOVAR, Artemis, EMBOSS Transeq, SnapGene Viewer, GATK, CLC Genomics Workbench, SeqMan Ngen |
| Sex Determination from Genomic Data | FindZX, Sex.DetERRmine, Peddy, PLINK, |
| Gene Name Errors | GeneNameErrors2020, Gene Updater |
| Bacterial genomes | Bacterial and Viral Bioinformatics Resource Center (BV-BRC), NCBI Bacterial Genomes, MicroScope, BacDive, JGI IMG, Ensembl Bacteria, BioCyc |
| Sequence Analysis | NCBI’s Conserved Domain Search, InterPro, UCSC Genome Browser, Bioconductor, EMBL-EBI’s Search and Sequence Analysis Tools |
| Microarray Data Analysis | GEOquery, ArrayExpress |
| Ontology Tools | OntoCheck, Protégé (which is compatible with the ontology reasoner HermiT), SNOMED CT Browser, UMLS Terminology Services, BioPortal, AberOWL, Ontobee, Ontology Lookup Service (OLS), BioBert |
| Quality Assurance of Data | FastQC, MultiQC, Trim Galore!, Picard Tools, SAMtools, Cell Ranger, Seurat, SCANPY |
| Workflow Management | Galaxy, Snakemake, Nextflow, Toil, Taverna, Terra.bio, Apache Hadoop |
a
more details in supplemental excel Table 2