mixtureS: a novel tool for bacterial strain reconstruction from reads
mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, witho...s and the vast majority of experimental datasets. Availability The source code a...1408 days ago
chromatiblock: Scalable, whole-genome visualisation of structural changes in prokaryotes
To create a fresh environment for chromatiblock to run in do: conda create --name chromatiblock conda activate chromatiblock conda install chromatiblock --channel co...1405 days ago
G-NEST: The Gene NEighborhood Scoring Tool
The Gene NEighborhood Scoring Tool (G-NEST) combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all window sizes. Primary author of final code = William F. Martin. Example data files are in the separate repository.1372 days ago
Updated science-wide author databases of standardized citation indicators
There was great interest in the databases of standardized citation metrics across all scientists and scientific di...g the single calendar year 2019 (Table-S7-singleyr-2019). Updated databases and code a...1321 days ago
CoverM: Read coverage calculator for metagenomics
CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications. CoverM calculates cove...1156 days ago
AutoGluon: AutoML for Text, Image, and Tabular Data
AutoGluon automates machine learning tasks enabling you to easily achieve strong predictive performance in your applications. With just a few lines of code, you can train and deploy high-accuracy machine learning and deep learning models on text, image, and tabular data.1269 days ago
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MMseqs2: ultra fast and sensitive sequence search and clustering suite
MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs...achieves almost the same sensitivity. It can perform profile searches with the same sensitivity a...1258 days ago
Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
Ktrim is written in C++ for GNU Linux/Unix platforms. After uncompressing the source package, you can find an executable file ktrim under ...1233 days ago