GEAR Genomics: a user-friendly, open-source web platform enabling interactive genomic analysis for molecular biologists
This repository provides a GEAR web application snapshot for all the tools included in the publication and deposited on Zenodo.
The GEAR web applications are hosted at https://www.gear-genomics.com/ with the following App URLs.
| App URL | Purpose | Input(s) | Output(s) | Backend service |
|---|---|---|---|---|
| /alfred/ | Sequencing QC | JSON | Visualization of QC results | Alfred CLI |
| /bgen/ | Sequencing barcode generator | Number of barcodes and length | Set of barcodes | Client-only |
| /bistro/ | Barcode diversity | Barcode sequences | Visualization of barcode distribution | Client-only |
| /halo/ | Genomic haplotype viewer | JSON | Visualization of Strand-Seq data | Halo CLI |
| /indigo/ | Chromatogram variant calling | Trace file | Single-nucleotide variants and InDels | Tracy |
| /maze/ | Sequence alignment | Two DNA sequences | Dotplot visualization | Client-only |
| /padlock/ | Padlock probe design for ISS | Probe design parameters | Designed probes, UCSC links | Dicey |
| /pearl/ | Sanger chromatogram assembly | Trace files, reference genome | Trace assembly | Tracy |
| /primer3plus/ | Design primers for a DNA sequence | Primer design parameters | Picked primers | Primer3 |
| /rdml-tools/ | Tools to analyze qPCR data | RDML file(s) | RDML analysis results | RDML-Python |
| /sabre/ | Sequence alignment browser | MSA in FASTA format | MSA browser | Client-only |
| /sage/ | Sanger chromatogram alignment | Trace file, reference genome | Interactive alignment viewer | Tracy |
| /salt/ | Sequence alignment computation | Two DNA sequences | Sequence alignment | Client-only |
| /silica/ | In-silico PCR | Primer sequences, genome | Amplicon and primer hits | Dicey |
| /teal/ | Trace file viewer | Trace file | Interactive viewer | Tracy |
| /wally/ | NGS alignment plotter | BAM/CRAM file | Alignment plot | Wally |
| /wily-dna-editor/ | DNA manipulation | DNA sequence | DNA editor | Client-only |
Abbreviations: QC: Quality control, CLI: Command-line interface, InDels: Insertions and Deletions, MSA: Multiple sequence alignment, ISS: In situ sequencing
The software tarballs are in the software subdirectory.