dib-lab / 2018-ncbi-lineagesLinks
Extract lineage CSVs from NCBI for use with sourmash lca.
☆29Updated 2 years ago
Alternatives and similar repositories for 2018-ncbi-lineages
Users that are interested in 2018-ncbi-lineages are comparing it to the libraries listed below
Sorting:
- Metagenomic species profiling with enhanced coverage of the human gut microbiome☆25Updated last year
- PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied ann…☆24Updated 2 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- Protein Alignment and Detection Interface☆60Updated last year
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆50Updated 3 years ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 7 years ago
- Locus and lineage tests for bacterial GWAS☆29Updated 8 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 3 years ago
- Metagenomic profiling and phylogenetic distances via common kmers☆42Updated 4 years ago
- VIRULIGN: fast codon-correct alignment and annotation of viral genomes☆35Updated 4 years ago
- De novo Extraction of Strains from MetAgeNomes☆71Updated 5 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 6 years ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆31Updated last year
- Database of genomes integrated from the gut microbiome and other environments☆44Updated 2 years ago
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆25Updated 2 years ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆27Updated 7 years ago
- Gene-flank analysis tool☆34Updated 11 months 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
- A resistome profiler for Graphing Resistance Out Of meTagenomes☆65Updated 5 years ago
- Scalable creating/updating of metagenome profiling databases☆62Updated 5 months ago
- kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding☆23Updated 2 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- Strain Resolution ON Graphs☆49Updated 2 years ago
- Assembling the cause of phenotypes and genotypes from NGS data☆29Updated 5 years ago
- Split Kmer Analysis☆65Updated 3 years ago
- Tool for quick offline batch conversion of Genbank IDs or accessions to taxonomy strings☆14Updated last year
- A nextflow pipeline for decontamination of short reads, long reads and contigs☆55Updated 5 months ago
- Visualize whole genome alignments as linear maps☆74Updated 4 months ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆39Updated 9 months ago
- Influenza genome analysis Nextflow workflow☆24Updated 2 months ago