DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
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Updated
Mar 9, 2024 - Python
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
Quickly search, compare, and analyze genomic and metagenomic data sets.
Fast k-mer based tool for multi locus sequence typing (MLST)
Predict plasmids from uncorrected long read data
🎯 Generate DNA sequences with specified amino acid, codon, and k-mer frequencies
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.
FOCUS: An Agile Profiler for Metagenomic Data
instructions, python and R code for generating lava lamp plots of kmer coverage
Collapse a set of redundant kmers to use IUPAC degenerate bases
Get exons from a transcriptome and raw genomic reads using abyss-bloom and bedtools
ALTEMO is a package of functions written in Python for bioinformatics proposed as a final project in the course of Algorithmic Techniques and Models (325) at the University of Málaga.
K-Mer management tools
A program to read sequences from fastq file and find out the frequency of all substrings with length k across all sequences in the file.
Repo for code and data related to project developing methodology for applying Harmonic Mean P-Values to sliding windows of multiple aligned genomes.
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