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Search results for python kmer
kmer
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python
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9 search results found
Khmer
⭐
729
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
Dnabert
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471
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
Sourmash
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431
Quickly search, compare, and analyze genomic and metagenomic data sets.
Pyseer
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81
SEER, reimplemented in python 🐍🔮
Ganon
⭐
73
ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
Poppunk
⭐
71
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
Kover
⭐
47
Learn interpretable computational phenotyping models from k-merized genomic data
Subphaser
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40
Phase, partition and visualize subgenomes of an allopolyploid or hybrid based on the subgenome-specific repetitive kmers.
Charcoal
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31
Remove contaminated contigs from genomes using k-mers and taxonomies.
Prophyle
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30
Accurate, resource-frugal and deterministic DNA sequence classifier.
Strainscan
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30
High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers
Stringmlst
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27
Fast k-mer based tool for multi locus sequence typing (MLST)
Tiptoft
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20
Predict plasmids from uncorrected long read data
Kgwasflow
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19
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
Mof Search
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18
BLAST-like search across all pre-2019 bacteria on ordinary laptop and desktop computers within a few hours
Virstrain
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16
An RNA virus strain-level identification tool for short reads.
Freqgen
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16
🎯 Generate DNA sequences with specified amino acid, codon, and k-mer frequencies
Kmerdb
⭐
10
Python bioinformatics CLI for k-mer count distribution and transition probabilities.
Castor_krfe
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9
Alignment-free method to identify and analyse discriminant genomic subsequences within pathogen sequences
Miniphy
⭐
7
Phylogenetic compression of extremely large genome collections [661k ↘𝟏𝟕.𝟓𝐆𝐁, BIGSIdata ↘𝟓𝟐 𝐆𝐁]
Localhgt
⭐
6
Detect complete HGT event rapidly and accurately from complex metagenomics data
Lavalampplot
⭐
6
instructions, python and R code for generating lava lamp plots of kmer coverage
Focus
⭐
5
FOCUS: An Agile Profiler for Metagenomic Data
Circrna_tools_comparison
⭐
5
This repository contains the results and comparison visualization of circRNA candidates detected by circRNA prediction softwares.
Panfeed
⭐
5
A k-mer counter that streams gene-cluster specific k-mers, while keeping k-mer positional information. Useful for microbial GWAS analyses with higher interpretability.
Fastas2kmers
⭐
5
A naive implementation of a k-mer counter in Python, takes fasta files and k-mer length requests and outputs all k-mers of length k, their reverse complement, and their frequency within their respective sequence for each sequence in the file.
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