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Lists (8)
aDNA
1 repository
Ecology analysis
Spatial analysis etc.4 repositories
Evolution analysis
1 repository
General usage
5 repositories
Genome assembly
Genome assembly, assessment, annotation tools25 repositories
Phylogenetics
14 repositories
Plot, ref manage, writing
5 repositories
Popgen
18 repositories
Starred repositories
This repo includes ChatGPT prompt curation to use ChatGPT and other LLM tools better.
The second version of the Kraken taxonomic sequence classification system
Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis
Tools for data handling and analysis in macroecology
An R package for the calculation of taxonomic, phenotypic and phylogenetic metrics across grid cells.
Phylogenetic orthology inference for comparative genomics
Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
C++ API & command-line toolkit for working with BAM data
Simulators of spatial genetic diversity: for non-programmers and researchers!
Software to construct and analyse KewTreeOfLife (PAFTOL project)
A structural variation pipeline for short-read sequencing
A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
deep learning prediction of geographic location from individual genome sequences
A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - for sampled individuals, and for pool sequencing.
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Pipelines and tools for the processing of ancient and modern HTS data.
RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
Transcript assembly and quantification for RNA-Seq
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Aggregate results from bioinformatics analyses across many samples into a single report.
This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster
iTerm2 is a terminal emulator for Mac OS X that does amazing things.