Pinned Repositories
2015-biogas-cebitec
Bremges et al. (2015). GigaScience, 4:33.
2015-pseudo
kgrep
Roughly speaking, a 'grep' for k-mers
MeCorS
Metagenome-enabled error correction of single cell sequencing reads
NanoSim
Nanopore sequence read simulator
sc
traitar
CAMISIM
CAMISIM: Simulating metagenomes and microbial communities
EMDUnifrac
Computation of Unifrac using Earth Movers Distance
2015-biogas-cebitec
Bremges et al. (2015). GigaScience, 4:33.
abremges's Repositories
abremges/kgrep
Roughly speaking, a 'grep' for k-mers
abremges/MeCorS
Metagenome-enabled error correction of single cell sequencing reads
abremges/NanoSim
Nanopore sequence read simulator
abremges/TreeHugger
Phylogenetic assignment and tree inference using defined marker gene sets
abremges/abremges.github.io
Personal homepage
abremges/academicpages.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
abremges/CAMIProfilingTools
A collection of scripts for manipulating CAMI profiling files
abremges/checkm-genome
abremges/ClonalFrameML
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
abremges/docker-unicycler
Docker container for the Unicycler hybrid assembler
abremges/fermi
abremges/ggjoy
Geoms to make joy plots using ggplot2
abremges/INNUca
INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search
abremges/kd-tree-evaluation
abremges/LRSIM
10x Genomics Reads Simulator
abremges/Mash
Fast genome and metagenome distance estimation using MinHash
abremges/minia
Minia is a short-read assembler based on a de Bruijn graph
abremges/ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
abremges/nextflow
A DSL for data-driven computational pipelines
abremges/rfc
Request for comments on interchangeable bioinformatics containers
abremges/Roary
Rapid large-scale prokaryote pan genome analysis
abremges/Scoary
Pan-genome wide association studies
abremges/shellcheck
ShellCheck, a static analysis tool for shell scripts
abremges/shields
Shields badge specification, website and default API server
abremges/snowball
abremges/spades
SPAdes Genome Assembler http://cab.spbu.ru/spades
abremges/spades-1
abremges/tutorials
In this repo you will find demos and tutorials prepared by members of the CBIB. Feel free to use them for non-commercial activities given that you give proper credit. Have fun!
abremges/Unicycler
hybrid assembly pipeline for bacterial genomes
abremges/x