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accnet

alphafold

Open source code for AlphaFold.

bigsdb

Bacterial Isolate Genome Sequence Database (BIGSdb) - A platform for gene-by-gene bacterial population annotation and analysis.

bio-tradis

A set of tools to analyse the output from TraDIS analyses

bowtie2

A fast and sensitive gapped read aligner

clonalframeml

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

cronobacter_specific_features

supplementary materials of Cronobacter genus or species specific features

crotrait

A portable tool for in silico species identification, serotyping and multilocus sequence typing of Cronobacter genus

cufflinks

cutadapt

Cutadapt removes adapter sequences from sequencing reads

fastani

Fast Whole-Genome Similarity (ANI) Estimation

fqgrep

An approximate sequence pattern matcher for FASTQ/FASTA files.

ggtree

:christmas_tree:Visualization and annotation of phylogenetic trees

ggtreeextra

:lemon: Add Geom Layers On Circular Or Other Layout Tree Of “ggtree”

hosts

:statue_of_liberty:最新可用的google hosts文件。镜像：

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

isescan

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome

ls-bsr

Large scale Blast Score Ratio (BSR) analysis

minced

Mining CRISPRs in Environmental Datasets

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

orthofinder

Phylogenetic orthology inference for comparative genomics

pgap

NCBI Prokaryotic Genome Annotation Pipeline

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

rbaps

R implementation of the BAPS software for Bayesian Analysis of Population Structure

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

soapdenovo2

Next generation sequencing reads de novo assembler.

splitthreader

Explore rearrangements and copy-number amplifications in a cancer genome

tn-seq

trimgalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

trimmomatic