maximilianh / multiSubLinks
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 directory and merges everything into a single output directory. Auto-detects input file formats. Can submit the results to multiple repositories from the command line.
☆36Updated 3 years ago
Alternatives and similar repositories for multiSub
Users that are interested in multiSub are comparing it to the libraries listed below
Sorting:
- Bioinformatics Pipeline and Visualization resources☆58Updated last year
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Updated last month
- SARs-CoV-2 Primer schemes☆16Updated 5 months ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆41Updated last year
- Webin command line submission program.☆34Updated 2 weeks ago
- Pipeline to generate NGS reads from a phylogeny☆39Updated 3 years ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆56Updated last week
- Split Kmer Analysis☆65Updated 3 years ago
- ☆36Updated 6 months ago
- This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.☆58Updated 6 months ago
- de novo virus assembler of Illumina paired reads☆57Updated 4 years ago
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆48Updated 2 months ago
- INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…☆38Updated this week
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆56Updated this week
- Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)☆56Updated 2 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 4 years ago
- Primer schemes for real-time genome epidemiology☆29Updated 2 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago
- SC2 variant detection and composition pipeline☆17Updated 2 years ago
- ☆84Updated 2 years ago
- Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.☆43Updated 2 months ago
- Influenza data pipeline to automate genotyping assignment☆37Updated 4 months ago
- Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.☆49Updated 3 years ago
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆39Updated 2 weeks ago
- A scalable bacterial genome assembly, annotation and analysis pipeline☆74Updated last year
- ARTIC SARS-CoV-2 workflow and reporting☆50Updated 5 months ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆41Updated last week
- A tool for removing redundant genomes from a set of assemblies☆77Updated last month
- Benchmark datasets for WGS analysis☆39Updated 6 years ago
- Split k-mer analysis – version 2☆92Updated 2 months ago