esteinig / scrubby
Host depletion optimised for clinical metagenomic sequencing applications
☆14Updated this week
Related projects: ⓘ
- Shared k-mer content between two genomes☆17Updated last year
- k-mers and the like☆14Updated this week
- software to identify primers that can distinguish genomes☆14Updated this week
- BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons☆12Updated this week
- Drug Resistance Prediction with Reference Graphs☆19Updated last year
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆17Updated last week
- Iterate over minimizers of a DNA sequence☆24Updated 2 months ago
- Just another minhash implementation.☆12Updated 3 weeks ago
- Experiments with using BIGSI data structure for metagenomic and QC applications☆18Updated last month
- MetagenOmic read Re-Assigner and abundance quantifier☆17Updated 3 months ago
- ☆10Updated last year
- Python implementation of barrnap (Bacterial ribosomal RNA predictor)☆13Updated last week
- Visualize microbial evolution at the SNP level!☆10Updated last month
- A rust wrapper for the spoa C++ partial order alignment library☆10Updated 2 months ago
- A taxonomic classifier for shotgun metagenomics reads☆12Updated 6 months ago
- Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.☆22Updated 11 months ago
- fast, multithreaded sourmash operations: search, compare, and gather.☆15Updated this week
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆28Updated 3 weeks ago
- A FASTA/FASTQ format parser library☆20Updated 6 months ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆20Updated 3 months ago
- A long read simulator based on badread idea☆20Updated last year
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆15Updated 4 months ago
- metagenome population recombination rate estimation pipeline☆12Updated last month
- Non-redundant pangenome assemblies from multiple genomes or bins☆13Updated last month
- Robust individual and aggregate checksums for nucleotide sequences☆16Updated 9 months ago
- Extracts subgraphs or components from a graph in GFA format☆21Updated 3 months ago
- Minimum plain text representation of kmer sets☆16Updated 3 weeks ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆30Updated last week
- Next Index to Query Kmer Intersection☆16Updated last year
- Variant call verification☆14Updated last year