vikash84's Projects
Taxonomic classification of viruses at Order and Family level
Dengue virus genotyping from shotgun and targeted metagenomicsโ - A nextflow pipeline
DDBJ Fast Annotation and Submission Tool
Viral genome annotation and data submission tool to DDBJ
Trivial DIAMOND + ORF calling workflow
Materials for the Dickson Lab SOP for Analysis of 16S rRNA Gene Amplicon Data
discover-virome: identify and quantify viruses from metagenomic assemblies
Tool for analysing viral diversity from High Throughput Sequencing
Quantify viral genetic diversity within hosts from NGS data (paired-end raw reads) without needing to reconstruct full-length haplotypes.
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
Nextflow/Docker pipelines for "easy use"
Automated monitoring and logging of sequencing runs performed on the GridION sequencer.
Pipelines for Drosophila genome assembly and analysis
Learning resources originally for a class held December 2020 "Dry bench skills for Researchers". Expanding based upon mini-courses.
RNA-seq tutorial
EasyBuild - Singularity tutorial
Pipeline to automatically analyse SARS-CoV-2 Whole genome sequencing Illumina data obtained using EasySeq SARS-CoV-2/COVID-19 Whole Genome Sequencing kit.
16S amplicon NGS - Hands-on
Fast genome-wide functional annotation through orthology assignment
Assembly based core genome SNP alignments for bacteria
Python code to perform email related tasks and analyze email data
A quick workflow to get researchers started with the bioinformatic pipeline used in the Environmental Metagenomics program.
A pipeline and a framework for NGS analysis (RNA-Seq and soon Chip-Seq)
Prediction of B-cell epitopes from amino acid sequences using deep neural networks.
Prediction of B-cell epitopes from amino acid sequences using deep neural networks.
Small script to use ABRicate output to extract genes from genome assemblies, reverse complement if necessary, and print to a file
A tool to infer metagenomic sample composition