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An efficient way to convert gff3 annotation files into EMBL format ready to submit.
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.
Collecting Genotypes from ENA and make their SNPs
TSV and XLSX templates for submitting ENA objects (study, experiment, sample and run) using the ENA-upload-tool
Snakemake workflow to upload Sars-Cov-2 reads to ENA
血小板转录组fastq数据处理
Query the ENA for different types of data and bulk download
R functions and workflow for submitting amplicon sequence data to the ENA.
Source codes of API queries in R (made available together with datasets) of Medical Translation in the History of Modern Genomics (TRANSGENE)
Dresser-un-fonctionnaire.com