fedarko / strainFlye
Pipeline for analyzing (rare) mutations in metagenome-assembled genomes
☆11Updated 4 months ago
Alternatives and similar repositories for strainFlye:
Users that are interested in strainFlye are comparing it to the libraries listed below
- Scalable and High Performance Variant Calling on Cluster Environments☆10Updated 2 years ago
- Robust individual and aggregate checksums for nucleotide sequences☆16Updated last year
- SeqWho - A reliable and rapid FASTQ(A) file classifier☆11Updated 2 years ago
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆26Updated last year
- Hierarchical binned indexed data store for on-disk genomic data.☆14Updated this week
- Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.☆22Updated last year
- ☆16Updated 6 years ago
- A k-mer search engine for all Sequence Read Archive public accessions☆19Updated 2 months ago
- This is the codebase for Faucet, described in our manuscript: https://academic.oup.com/bioinformatics/article/34/1/147/4004871, by Roye R…☆18Updated 7 years ago
- Genome assembly quality improvement assisted by alternative assemblies and paired-end Illumina reads☆7Updated 6 years ago
- Repository for codes, analyses and visualizations for the CAMI II challenges☆11Updated last year
- RabbitMash: an efficient highly optimized implementation of Mash.☆21Updated last year
- Highly sensitive pathogen detection☆11Updated 4 years ago
- ☆15Updated 4 years ago
- Next Index to Query Kmer Intersection☆16Updated last year
- Coronavirus (SARS-Cov-2) sequencing analysis☆10Updated 3 years ago
- Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.☆20Updated last week
- A script to extract graph structure from multiple sequence alignment result and output as GFA/JSON for vg☆11Updated 5 years ago
- ☆15Updated last year
- software to identify primers that can distinguish genomes☆20Updated 2 months ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated last year
- Minimum plain text representation of kmer sets☆17Updated 4 months ago
- easy_sbatch - Batch submitting Slurm jobs with script templates☆17Updated 3 years ago
- Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment☆16Updated 6 years ago
- Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…☆12Updated 7 months ago
- Variant call adjudication☆16Updated 7 months ago
- Non-redundant pangenome assemblies from multiple genomes or bins☆13Updated 5 months ago
- Hidden Markov Model based Copy number caller☆20Updated 2 months ago
- Rapid discovery of reciprocal best blast pairs.☆10Updated 2 months ago
- k-mers and the like☆20Updated this week