Genesis's repositories
Mitogenome_assemblies
Scripts used for assembly and analysis of the mitochondrial genome of the meerkat (Suricata suricatta)
AnnelidaMitoGenomes
This repository contains the scripts used to conduct the analyses of annelid mitochondrial genomes. The description how the scripts have been used can be found in the paper itself.
bio
Bioinformatics utilities.
biofx_python
Code for Mastering Python for Bioinformatics (O'Reilly, 2021, ISBN 9781098100889)
biostar-central
Biostar Q&A
biostar-handbook
Issue tracker for the Biostar Handbook
bsa
Bulked-Segregant Analysis using vcf file with or without parents
BSATOS
Bulked segregation analysis tools for outbreeding species(BSATOS)
ColabFold
Making Protein folding accessible to all!
DeepBSA
DeepBSA is a novel bulked segregant analysis (BSA) software for the dissection of complex traits.
eKLIPse
a tool for predicting mitochondrial DNA deletions using soft-clipping
EVidenceModeler
source code for EVM
hifisr
HiFi-SR is a Python-based pipeline for the detection of plant mitochondrial structural rearrangements based on the mapping of PacBio high-fidelity (HiFi) reads or Circular Consensus Sequencing (ccs) data, to a reference genome (i.e., the hypothetical master cycle DNA).
MEANGS
MitoDNA extending assembler from NGS data
Mito-Hacker
Cellular Mitochondrial Analysis
MitoCap
An R package for processing high-throughput sequence data from raw reads to alignments from mitochondrial genomes sequenced as by-catch
mitocorrect
Automatically correct your mitochondrial genome annotations using expert knowledge
MutMap
MutMap pipeline to identify causative mutations responsible for a phenotype
OGAP
OGAP: Organelle Genome Annotation Pipeline
OrthoFinder
Phylogenetic orthology inference for comparative genomics
practical-statistics-for-data-scientists
Code repository for O'Reilly book
recycle
Obtain the mitochondrial or chlorophyll sequence from the reads of genome sequencing, and perform assembly.
sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
tiny_python_projects
Code for Tiny Python Projects (Manning, 2020, ISBN 1617297518). Learning Python through test-driven development of games and puzzles.