BU-ISCIII / SARS-Cov2_analysis
Documentation for analyzing SARS-Cov2 samples.
☆11Updated 4 years ago
Alternatives and similar repositories for SARS-Cov2_analysis:
Users that are interested in SARS-Cov2_analysis are comparing it to the libraries listed below
- kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding☆23Updated last year
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Output FASTQ summary statistics in JSON format☆29Updated 2 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆41Updated 4 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated 2 years ago
- Read contamination removal☆25Updated last year
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆24Updated 6 months ago
- Collection of R scripts for SARS-CoV-2 (variant) analyses☆12Updated 2 years ago
- Masks recombinant regions in an alignment based on ClonalFrameML output☆10Updated 6 years ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Predict MLST directly from uncorrected long reads☆27Updated 3 years ago
- strain-level analysis tools☆36Updated 6 months ago
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆18Updated 9 years ago
- Code to create a PRG from a Multiple Sequence Alignment file☆25Updated last year
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆21Updated last year
- Intra-species bacterial contamination detection☆25Updated 2 months ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated 2 years ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆27Updated 7 years ago
- ☆26Updated last year
- Strain Prediction and Analysis with Representative SEquence☆18Updated 4 months ago
- QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run☆11Updated 4 months ago
- Gene-flank analysis tool☆27Updated 4 months ago
- Quantifying the significance of genetic variation using probabilistic profile-based methods.☆19Updated 4 years ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Updated 4 months ago
- An `R` package for various phylogenetic and evolutionary biology data manipulations☆12Updated 7 years ago
- A method of assessing sequence complexity based on kmer frequencies☆32Updated 7 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Colinear block visualisation tool☆30Updated last year
- Influenza genome analysis Nextflow workflow☆22Updated 3 weeks ago