chanzuckerberg / czid-cli
CZID (formerly IDseq) infectious disease command-line interface
☆21Updated 6 months ago
Alternatives and similar repositories for czid-cli:
Users that are interested in czid-cli are comparing it to the libraries listed below
- A Nextflow full-length 16S profiling pipeline for ONT reads☆24Updated last year
- Bioinformatics Pipeline and Visualization resources☆55Updated 5 months ago
- ☆12Updated 5 years ago
- Split Kmer Analysis☆63Updated 2 years ago
- Pan-Genomic Matching Statistics☆48Updated 9 months ago
- hecatomb is a virome analysis pipeline for analysis of Illumina sequence data☆57Updated 2 weeks ago
- Snakemake workflow for metagenomic classification with Kraken2☆65Updated last year
- A scalable bacterial genome assembly, annotation and analysis pipeline☆71Updated last year
- Influenza genome analysis Nextflow workflow☆24Updated 3 weeks ago
- Microbiome classification pipeline☆64Updated 9 months ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆73Updated 5 months ago
- Primer schemes for real-time genome epidemiology☆27Updated last year
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆27Updated last year
- Standard database for the TBProfiler tool☆29Updated last month
- Precise host read removal. Friendly to microbes, hostile towards host☆84Updated last month
- Fast k-mer based tool for multi locus sequence typing (MLST)☆43Updated 4 years ago
- This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…☆58Updated 3 years ago
- Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…☆35Updated 2 years ago
- Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.☆35Updated 4 months ago
- FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomi…☆66Updated 2 weeks ago
- a collection of scripts for organising bacterial genomes by species☆76Updated 2 years ago
- Snakemake pipeline for simulating shotgun metagenomic samples☆22Updated last week
- Nextstrain build for avian influenza viruses☆22Updated last week
- Adapter trimmer for Oxford Nanopore reads using ab initio method☆39Updated 2 months ago
- IS mapping software☆53Updated 3 years ago
- ☆79Updated last year
- ARTIC SARS-CoV-2 workflow and reporting☆50Updated last month
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆45Updated last year
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆93Updated this week
- Protein Alignment and Detection Interface☆61Updated 9 months ago