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16s_tutorial

2014-5-metagenomics-workshop

Metagenomics Workshop 2014-5-21 to 2014-5-23 at SciLifeLab, Stockholm

2016

Materials prepared by the instructors of the #NGSchool2016

2016-tutorials

repo for 2016 EDAMAME tutorials

2017

Materials used during #NGSchool2017

alitv

Visualize whole genome alignments as linear maps

angus

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

annocript

Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission. It gives information about the longest ORF (using DNA2PEP) and non-coding potential of the sequences (using Portrait). A final heuristic makes Annocript able to identify putative long non-coding RNAs among your transcripts. Like our facebook page to be always updated: https://www.facebook.com/annocript

apt-cyg

Apt-cyg, an apt-get like tool for Cygwin

assembly_improvement

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

atsphere_cc

scripts to reproduce the analysis and figures from Bai et al., Nature, 2015

atsphere_wgs

scripts to reproduce the analysis and figures from Bai et al., Nature, 2015

awesome-public-datasets

An awesome list of high-quality datasets in public domains (on-going).

bac-genomics-scripts

Collection of scripts for bacterial genomics

bacmet-database

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bioattribution

bioconda-recipes

Conda recipes for the bioconda channel.

biodiversityr

:exclamation: This is a read-only mirror of the CRAN R package repository. BiodiversityR — Package for Community Ecology and Suitability Analysis. Homepage: http://www.r-project.org, http://www.worldagroforestry.org/resources/databases/tree-diversity-analysis

bioinformatics-toolbox

Multi-purpose bioinformatics toolbox

bioinformatics_scripts

Just a bunch of scripts I use for bioinformatics -- feel free to use, reuse, and improve

bioinformatics_scripts-1

Scripts UBC

biostar-tutorials

Code for biostar tutorials - mostly R and Perl

blasr

BLASR: The PacBio® long read aligner

blastdbget

Download Blast databases from ftp.ncbi.nlm.nih.gov/blast/db, validate, and extract.

checkm

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

chommeta

scripts to reproduce the analysis and figures from Hacquard et al., Cell Host and Microbe, 2015

clonalframeml

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

co-occurrence

R scripts for performing co-occurrence analyses

cogmapper

This is a pipeline for finding out the COG (Cluster of Orthologous Groups) distribution for a list of bacterial genomes.