dib-lab / 2018-ncbi-lineagesLinks
Extract lineage CSVs from NCBI for use with sourmash lca.
☆29Updated last year
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:
- PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied ann…☆26Updated 2 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- Metagenomic species profiling with enhanced coverage of the human gut microbiome☆25Updated last year
- Metagenomic profiling and phylogenetic distances via common kmers☆42Updated 4 years ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 6 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆46Updated 2 years ago
- Locus and lineage tests for bacterial GWAS☆29Updated 7 years ago
- De novo Extraction of Strains from MetAgeNomes☆70Updated 5 years ago
- Split Kmer Analysis☆65Updated 3 years ago
- Quantifying the significance of genetic variation using probabilistic profile-based methods.☆19Updated 4 years ago
- Find Unique genomic Regions☆30Updated 3 months ago
- A method of assessing sequence complexity based on kmer frequencies☆32Updated 7 years ago
- ANNOgesic - A Swiss army knife for the RNA-Seq based annotation of bacterial/archaeal genomes☆31Updated last year
- Ley Lab MetaGenome Profiler DataBase generator☆50Updated 2 years ago
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆24Updated 2 years ago
- Protein Alignment and Detection Interface☆61Updated last year
- strain-level analysis tools☆38Updated 8 months ago
- In-depth characterization and annotation of differences between two sets of DNA sequences☆60Updated 5 years ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆29Updated last year
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 3 years ago
- Scalable creating/updating of metagenome profiling databases☆61Updated 3 weeks ago
- Improve the quality of a denovo assembly by scaffolding and gap filling☆57Updated 4 years ago
- MAG Circularization Method☆33Updated 3 years ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆49Updated 2 years ago
- Detection of NCLDV signatures in 'omic data☆35Updated last year
- A pipeline for performing genome-wide association tests for bacterial genomes.☆27Updated 7 years ago
- Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to constr…☆33Updated last year
- 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
- Gene-flank analysis tool☆28Updated 6 months ago