Pyrodigal
Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes - Published in JOSS (2022)
Phylen
Phylen: automatic phylogenetic reconstruction using the EggNOG database - Published in JOSS (2018)
genome-spy
A visualization grammar and GPU-accelerated toolkit for genomic data
codonu
A python project for analysis of codon usage for gene or genome analysis
karyoploteR
karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
genomeskim
QC and filtering of genome skims, followed by organelle assembly and/or genome analysis
https://github.com/althonos/pyaragorn
Cython bindings and Python interface to ARAGORN, a (t|mt|tm)RNA gene finder.
LTRpred
LTRpred: de novo annotation of intact retrotransposons - Published in JOSS (2020)
https://github.com/broadinstitute/gatk
Official code repository for GATK versions 4 and up
https://github.com/bernatgel/regioner
An R/Bioconfuctor package for association analysis of genomic regions based on permutation tests
https://github.com/alexpreynolds/disjoint-windows
Build a list of high-scoring, non-overlapping intervals using sampling or scheduling methods
btllib
btllib: A C++ library with Python interface for efficient genomic sequence processing - Published in JOSS (2022)
https://github.com/ay-lab/dchic
dcHiC: Differential compartment analysis for Hi-C datasets
sars-cov-2-sequenzdaten_aus_deutschland
Ein zentraler Bestandteil einer erfolgreichen Erregersurveillance ist das Verständnis der Verbreitung eines Erregers sowie seiner pathogenen Eigenschaften. Hierbei stellt das Wissen über das Erregergenom eine wichtige Informationsquelle dar. So erlaubt der Nachweis von Mutationen im Genom eines Erregers, Verwandtschaftsbeziehungen zu rekonstruie...
sammyseq
Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
https://github.com/brentp/mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
references
nf-core/references is a bioinformatics pipeline that build references, for multiple use cases
https://github.com/ampliconsuite/ecsimulator
Simulate ecDNA structures with user-specified properties.
GenomAutomorphism
An R package to compute the autimorphisms between pairwise aligned DNA sequences represented as elements from a Genomic Abelian group as described in the paper [Genomic Abelian Finite Groups](https://www.biorxiv.org/content/10.1101/2021.06.01.446543v2)
ramen
Regional Association of Methylation variability with the Exposome and geNome (RAMEN) is an R package whose goal is to identify Variable Methylated Regions (VMRs) in microarray DNA methylation data. Additionally, using Genotype (G) and Environmental (E) data, it can identify which G, E, G+E or GxE model better explains this variability.
islandevolution.github.io
Source code for the Island biology, diversification, genome evolution lab