chanzuckerberg / czid-web
Infectious Disease Sequencing Platform
โ84Updated this week
Alternatives and similar repositories for czid-web:
Users that are interested in czid-web are comparing it to the libraries listed below
- Catalog of genomic indexes freely available from public cloudsโ59Updated 2 months ago
- Antimicrobial Resistance Identification By Assemblyโ173Updated last year
- SEER, reimplemented in python ๐๐ฎโ120Updated 5 months ago
- Pairwise SNP distance matrix from a FASTA sequence alignmentโ132Updated last year
- Fast genome analysis from unassembled short readsโ284Updated 11 months ago
- "Reads to report" for public health and clinical microbiologyโ139Updated last year
- Antibiotic resistance prediction in minutesโ107Updated 4 months ago
- ๐Scaffold genome sequence assemblies using linked or long read sequencing dataโ93Updated 4 months ago
- Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.โ140Updated last year
- Viral genomics analysis pipelinesโ192Updated 6 months ago
- Assembly and intrahost/low-frequency variant calling for viral samplesโ133Updated this week
- [MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore readsโ272Updated 2 years ago
- Modules to interface with tools used in Ensembl Gene Annotation Process and scripts to run pipelinesโ18Updated this week
- LongQC is a tool for the data quality control of the PacBio and ONT long reads.โ160Updated last year
- software tools for haplotype assembly from sequence dataโ217Updated last month
- A snakemake-based pipeline for assembling and polishing long genomes from long nanopore readsโ69Updated 3 years ago
- Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS dataโ114Updated last week
- Pan-genome wide association studiesโ191Updated 10 months ago
- NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore readsโ107Updated last year
- Novelty-inclusive microbial community profiling of shotgun metagenomesโ140Updated last week
- SALSA: A tool to scaffold long read assemblies with Hi-C dataโ183Updated 10 months ago
- Making whole bacterial genome sequencing data analysis easyโ103Updated 4 months ago
- A collection of scripts to assist in the retrieval of data from the ENA Browserโ81Updated last year
- A toolbox for pangenome analysis and threshold evaluation.โ94Updated 2 years ago
- Analysis components from Oxford Nanopore Researchโ93Updated 6 months ago
- Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundaโฆโ150Updated 3 months ago
- VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assembliesโ131Updated this week
- A fast whole-genome aligner based on de Bruijn graphsโ144Updated last month
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.โ142Updated 3 months ago
- breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is inteโฆโ159Updated 2 weeks ago