Nextstrain build for novel coronavirus SARS-CoV-2
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Updated
Aug 27, 2024 - Python
Nextstrain build for novel coronavirus SARS-CoV-2
Rapid large-scale prokaryote pan genome analysis
Pathogen NGS Documentary
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
A tool to circularize genome assemblies
Antimicrobial Resistance Identification By Assembly
Finds SNP sites from a multi-FASTA alignment file
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Repository containing lists of all published ancient metagenomic (and related) samples and libraries
A set of tools to analyse the output from TraDIS analyses
Scripts. config, and snakefiles for seasonal-flu nextstrain builds
Get assembly statistics from FASTA and FASTQ files
Improve the quality of a denovo assembly by scaffolding and gap filling
A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.
Python3 scripts to manipulate FASTA and FASTQ files
Nextstrain build for mpox virus
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