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2020-07-machine-learning-sib

Course material for the 2020-07-machine-learning course at SIB

ahrd

High throughput protein function annotation with Human Readable Description (HRDs) and Gene Ontology (GO) Terms.

aligngraph

Algorithm for secondary de novo genome assembly guided by closely related references

alphafold_pytorch

An implementation of the DeepMind's AlphaFold based on PyTorch for research

amos

A clone of the official AMOS git repo on sourceforge: https://sourceforge.net/projects/amos/

analyses_rna_seq

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

annotation_viewer

applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2018

atlas

ATLAS - Three commands to start analysing your metagenome data

augustus

Genome annotation with AUGUSTUS

bbmap

(Not Offical) BBMap short read aligner, and other bioinformatic tools.

bigsdb

Bacterial Isolate Genome Sequence Database

bioinformatics-course-2020

biovirushost

BioVirusHost: A simple Python interface to query the information from Virus-Host DB

bit

Bioinformatics Tools

blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

blobtools2

Redesigning BlobTools to support interactive data exploration

bulkvis

cafe

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

canu

A single molecule sequence assembler for genomes large and small.

cds_extractor

Script for extracting Coding DNA Sequence (CDS) values from a GB file.

chroma_clade

Combined visualisation of phylogenetic and sequence data. Please see 'release' tab for executables and documentation below

cloudbiolinux

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

cluster-picker-and-cluster-matcher

For all your cluster needs

cog

Scripts and steps for making a consolidated COG database file for tools like DIAMOND.

community_software_tools_for_ngs

compleasm

A genome completeness evaluation tool based on miniprot

complexheatmap

Make Complex Heatmaps

contigs_filter