Genesis's repositories

GSAT

Graph-based Sequence Assembly Toolkit

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MITGARD

Mitochondrial Genome Assembly

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Mitogenome_assemblies

Scripts used for assembly and analysis of the mitochondrial genome of the meerkat (Suricata suricatta)

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MitoZ

MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes

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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.

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bio

Bioinformatics utilities.

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biofx_python

Code for Mastering Python for Bioinformatics (O'Reilly, 2021, ISBN 9781098100889)

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biostar-central

Biostar Q&A

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biostar-handbook

Issue tracker for the Biostar Handbook

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bsa

Bulked-Segregant Analysis using vcf file with or without parents

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BSATOS

Bulked segregation analysis tools for outbreeding species(BSATOS)

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ColabFold

Making Protein folding accessible to all!

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DeepBSA

DeepBSA is a novel bulked segregant analysis (BSA) software for the dissection of complex traits.

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eKLIPse

a tool for predicting mitochondrial DNA deletions using soft-clipping

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EVidenceModeler

source code for EVM

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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).

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MEANGS

MitoDNA extending assembler from NGS data

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Mito-Hacker

Cellular Mitochondrial Analysis

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MitoCap

An R package for processing high-throughput sequence data from raw reads to alignments from mitochondrial genomes sequenced as by-catch

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mitocorrect

Automatically correct your mitochondrial genome annotations using expert knowledge

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MutMap

MutMap pipeline to identify causative mutations responsible for a phenotype

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OGAP

OGAP: Organelle Genome Annotation Pipeline

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OrthoFinder

Phylogenetic orthology inference for comparative genomics

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practical-statistics-for-data-scientists

Code repository for O'Reilly book

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recycle

Obtain the mitochondrial or chlorophyll sequence from the reads of genome sequencing, and perform assembly.

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sourmash

Quickly search, compare, and analyze genomic and metagenomic data sets.

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tiny_python_projects

Code for Tiny Python Projects (Manning, 2020, ISBN 1617297518). Learning Python through test-driven development of games and puzzles.

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