NGS Processing Pipelines for WGS and WES data
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Updated
Nov 11, 2019 - Python
NGS Processing Pipelines for WGS and WES data
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A comprehensive workflow for de novo assembly of whole-genome shotgun sequencing data using Velvet, followed by BLAST searches to analyze assembled contigs.
Whole genome sequencing (WGS) was combined with bioinformatics tools to investigate the epidemiology of Vibrio cholerae in the Philippines and in other cholera affected countries.
Curated lists of features for Mtb genomic analysis
Joint Genotyping in MIT Fraenkel Lab with ALS Genomics + 1000 Genomes Data
Workflow for biological validation of germline SNP and indel variant datasets.
Shortbread2 is a bioinformatics pipeline for identifying single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) from High-Throughput Next Generation Sequencing (NGS) data.
Converter for Swiss-Coordinates and WGS-Coordinates.
GATK WGS workflow
Supplementary materials for the article entitled: Novel Algorithms for PFGE Bacterial Typing: Number of Co-Migrated DNA Fragments, Linking PFGE to WGS Results and Computer simulations for Evaluation of PulseNet International Typing Protocols
Transcriptional variant verification to validate predicted variants from genomic data in expressed transcripts
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