bikmi Goto Github PK

amplicon

Statistics and visualization for amplicon data

binsanity

Unsupervised Clustering of Environmental Microbial Assemblies Using Coverage and Affinity Propagation

biopython-cn

Biopython Tutorial Chinese Translation

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

canu

A single molecule sequence assembler for genomes large and small.

cat

CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

centrifuge

Classifier for metagenomic sequences

cgview

CGView is a Java package for generating high-quality, zoomable maps of circular genomes.

checkm

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

das_tool

DAS Tool

diting

DiTing: A pipeline to infer and compare biogeochemical pathways in metagenomic data

drep

Rapid comparison and dereplication of genomes

eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

flye

De novo assembler for single molecule sequencing reads using repeat graphs

fmap

Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies

galah

More scalable dereplication for metagenome assembled genomes

intertidal-sediments

data analysis for ammonia oxdizers in intertidal sediments

jellyfish

A fast multi-threaded k-mer counter

kneaddata

Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.

last-genome-alignments

lja

lotus2

Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.

magphase

Phasing for metagenomics using PacBio long reads

metabolic

A scalable high-throughput metabolic and biogeochemical functional trait profiler

metachip

Horizontal gene transfer (HGT) identification pipeline

metaprism

Taxonomical and Functional Profiling for Shotgun Metagenomic Sequencing

microbiomestatplot

Interpretation and visualization of microbiome charts

miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

mmgenome

Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes

mmseqs2

MMseqs2: ultra fast and sensitive search and clustering suite