ncbi / pipelinesLinks
☆13Updated 7 years ago
Alternatives and similar repositories for pipelines
Users that are interested in pipelines are comparing it to the libraries listed below
Sorting:
- Antibiotic resistance predictions in minutes on a laptop☆50Updated 6 years ago
- PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied ann…☆25Updated 2 years ago
- benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.☆21Updated 7 years ago
- Get microbial sequence data easier and faster☆28Updated 6 years ago
- Influenza genome analysis Nextflow workflow☆24Updated 3 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 8 months ago
- Extract lineage CSVs from NCBI for use with sourmash lca.☆29Updated 2 years ago
- EMIRGE reconstructs full length ribosomal genes from short read sequencing data.☆37Updated 2 years ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 7 years ago
- Assembling the cause of phenotypes and genotypes from NGS data☆29Updated 5 years ago
- De novo Extraction of Strains from MetAgeNomes☆71Updated 5 years ago
- A resistome profiler for Graphing Resistance Out Of meTagenomes☆65Updated 5 years ago
- Benchmark datasets for WGS analysis☆39Updated 6 years ago
- de novo virus assembler of Illumina paired reads☆58Updated 4 years ago
- VIRULIGN: fast codon-correct alignment and annotation of viral genomes☆35Updated 4 years ago
- Efficient and comprehensive metadata acquisition from the NCBI databases (includes SRA).☆50Updated 3 years ago
- Multilocus sequence typing by blast using the schemes from PubMLST☆30Updated 3 years ago
- The MLST pipeline developed by the PathOGiST research group☆36Updated 2 years ago
- Toolkit for preparing genomes for submission to NCBI☆29Updated 4 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…☆36Updated 3 years ago
- Bioinformatics Pipeline and Visualization resources☆60Updated last year
- Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.☆32Updated last month
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 5 years ago
- Predict plasmids from uncorrected long read data☆41Updated last month
- Protein Alignment and Detection Interface