Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing

Python package to study microbial communities using metabolic modeling.

Environmental growth media for MICOM.

Materials and presentation for the 2022 ISB Microbiome course.

CarveMe: genome-scale metabolic model reconstruction

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

R package for MetaboAnalyst

Variational autoencoder for metagenomic binning

Script to automatically create and run IGV snapshot batchscripts

A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.

MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

A collection of gcc tips. 100 maybe just mean many here.

Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"

A comparison of different Oxford Nanopore basecallers

DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications

genomic alignment similarity search tool

A tool that generates a network of metagenomic samples positioned and with links according to the number of taxa shared

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

超级速查表 - 编程语言、框架和开发工具的速查表，单个文件包含一切你需要知道的东西 ⚡

Fast and accurately polish the genome generated by noisy long reads.

Frequently asked questions of community phylogenetics

A fuzzy Bruijn graph approach to long noisy reads assembly

Genome assembly evaluation tool

Fast and accurate de novo assembler for long reads

De novo assembler for single molecule sequencing reads using repeat graphs

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Themes for Bootstrap