Pinned Repositories
claranet4
Python client for Aranet4 CO2 sensors
cryptocurrency-tools
hostile
Precise host read removal
kindel
Indel-aware consensus for aligned BAM
konstel
Hash-based phonemic sequence identifiers
seqsum
Robust individual and aggregate checksums for nucleotide sequences
tictax
Streaming sequence classification with web services ✓📌
vespasian
Genome-scale detection of selective pressure variation
primer-schemes
Tiling PCR primer scheme definitions
bede's Repositories
bede/FastANI
Fast Whole-Genome Similarity (ANI) Estimation
bede/flanker
Gene-flank analysis tool
bede/phylovega
Interactive tree visualizations in Python (powered by Vega).
bede/PopPUNK
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
bede/primer-schemes-pvh
Primer schemes for real-time genome epidemiology
bede/read-it-and-keep
Read contamination removal
bede/runListCompare
Python 3 port of runListCompare
bede/sars2-seq-eval
Evaluation of SARS-CoV-2 sequencing protocols
bede/velo
bede/viridian_workflow
bede/wf-artic
ARTIC SARS-CoV-2 workflow and reporting
bede/automate-PAML-codeml
bede/CMash
Fast and accurate set similarity estimation via containment min hash
bede/diversity-scripts
bede/ffpopsim
FFPopSim is a collection of C++ classes and a Python interface for efficient simulation of large populations, in particular when the product of mutation rate and population size is larger than one. It consists of one library for individual-based simulations, and a complementary one for simulation of the entire genotype distribution. The latter is coded efficiently using Fast-Fourier Transforms to speed up recombination operations.
bede/latex-thesis-template
The files for the course in LaTeX for Theses at the University of Manchester.
bede/mummer
Mummer alignment tool
bede/nanolyse
Remove lambda phage reads from a fastq file
bede/nasopharyngeal-virome
bede/northernbug.github.io
The NorthernBUG Website
bede/NucAmino
A nucleotide to amino acid alignment program optimized for virus gene sequences.
bede/OHSNAP
bede/pubtree
A hierarchical search tool for the Medline database
bede/pymummer
Python3 module for running MUMmer and reading the output
bede/SeqAnalTools
Command-line tools for analysing and manipulating sequence data, written for my own needs.
bede/siminf
Simulate coinfections of viral strains
bede/sparNA
Consensus assembly of deep sequenced RNA virus populations
bede/thesis-res
Thesis resources
bede/VESPA
VESPA: Very large-scale Evolutionary and Selective Pressure Analyses
bede/virmap