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☆56Updated 10 months ago
- SARs-CoV-2 Primer schemes☆16Updated 2 months ago
- Webin command line submission program.☆33Updated 2 weeks ago
- Split Kmer Analysis☆65Updated 3 years ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆41Updated 11 months ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆38Updated last month
- ☆53Updated 4 years ago
- SC2 variant detection and composition pipeline☆17Updated 2 years ago
- Phylogenetics between and within hosts at once, all along the genome.☆49Updated 9 months ago
- Pipeline to generate NGS reads from a phylogeny☆39Updated 2 years ago
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆38Updated 3 months ago
- Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.☆40Updated last month
- de novo virus assembler of Illumina paired reads☆56Updated 4 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆46Updated 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…☆59Updated 4 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 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 last year
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆54Updated this week
- Gene-flank analysis tool☆28Updated 6 months ago
- Efficient and comprehensive metadata acquisition from the NCBI databases (includes SRA).☆49Updated 3 years ago
- Reference-based consensus creation☆55Updated last week
- ASMNGS20 - 2020 Conference Details☆15Updated 3 years ago
- ARTIC SARS-CoV-2 workflow and reporting☆50Updated 2 months ago
- A Python library that exposes features from IQ-TREE - efficient software for phylogenomic inference☆29Updated this week
- This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.☆58Updated 3 months ago
- ☆26Updated last year
- Recombination-free trees☆58Updated 3 months ago
- A scalable bacterial genome assembly, annotation and analysis pipeline☆74Updated last year
- Adapter trimmer for Oxford Nanopore reads using ab initio method☆42Updated 7 months ago
- ☆36Updated 3 months ago