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2015-tutorials

tutorials for 2015 EDAMAME

2017-ucsc-metagenomics

Workshop materials for shotgun metagenomics

42-workshop

Workshop material for 42 PyCharm Tips and Tricks

abawaca

abawaca is a binning program for metagenomics

acetoscan

AcetoScan - Automated pipeline for the unsupervised analysis of FTHFS amplicon sequencing

agricolae

Statistical Procedures for Agricultural Research

akutils-v1.1.1

Mostly useful scripts and files for processing MiSeq amplicon data

alphafold

Open source code for AlphaFold.

altair

Declarative statistical visualization library for Python

amber

AMBER: Assessment of Metagenome BinnERs

amoa_miseq_sequencing

Existing tools based ‘assembly pipeline’ and ‘gap pipeline’ for paired-end MiSeq Illumina reads

amphora2

An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.

amplicon

Statistics and visualization for amplicon data

amplicon_based_metagenomics

data analysis scripts and pipline for NGS data: amplicon_based_metagenomics (e.g. 16S or functional marker gene)

ampvis2

ampvis2

anchor

angus

Materials for Analyzing Next-Generation Sequencing (ANGUS) course.

anhydeg

Database of anaerobic hydrocarbon degradation genes used for functional gene searching of metagenome data sets

anvio_owc_notes_liupf

remove contamination from MAGs, OWC wetland methanogens

art-r-translation

《R语言编程艺术》翻译项目文件

assembly_improvement

Improve the quality of a denovo assembly by scaffolding and gap filling

atlas

:earth_americas: ATLAS - workflows for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data.

awesome-python-books

:books: Directory of Python books

bacphlip

A python library for predicting phage lifestyle based on genome sequence

bamsplit

A efficient software tools to split Bam form all chromosome together to each chr one bam

bamtools

C++ API & command-line toolkit for working with BAM data

barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor

barrow_metagenome_scripts

Custom script accompanying Bowman and Deming, 2014, FEMS Microbial Ecology

basalt

basta

Basic Sequence Taxonomy Annotator