Scripts for going from raw .fastq files to processed and quality-checked .bam files for downstream analysis
☆14Nov 23, 2021Updated 4 years ago
Alternatives and similar repositories for data-processing
Users that are interested in data-processing are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Pipelines for analyzing genomic or transcriptomic data☆17Feb 29, 2024Updated 2 years ago
- GONE: Scripts, programs and an example data set☆54Jul 20, 2025Updated 9 months ago
- Analysis of genotyping and next-generation sequencing data in medical and population genetics☆23Aug 25, 2022Updated 3 years ago
- loco-pipe is an automated Snakemake pipeline that streamlines a set of essential population genomic analyses for low-coverage whole genom…☆31Jan 21, 2026Updated 3 months ago
- Bioinformatics pipeline to process whole genome resequencing data and perform genotype likelihood based population genomic analyses using…☆27Mar 20, 2026Updated last month
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.☆26Jan 5, 2026Updated 3 months ago
- Automated Rice Variant calling workflow for HPC, Cloud and Desktop systems.☆13May 11, 2024Updated last year
- ☆107Oct 14, 2021Updated 4 years ago
- Files for the the Physalia course on Population genomic inference from low-coverage whole-genome sequencing data, Oct 10-13, 2022☆72Oct 24, 2025Updated 6 months ago
- ☆47Mar 18, 2025Updated last year
- Population Genomics in R workshop☆12Mar 24, 2024Updated 2 years ago
- Fossil calibrations database☆16Sep 18, 2018Updated 7 years ago
- Course Materials for AAAGs 2018 Workshop☆13Aug 10, 2018Updated 7 years ago
- Course in population genomics at BiRC☆12Mar 18, 2026Updated last month
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- ☆16May 7, 2023Updated 2 years ago
- WinPCA. A package for windowed principal component analysis.☆49Apr 11, 2026Updated 2 weeks ago
- Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity☆18Mar 10, 2022Updated 4 years ago
- Process linked-read data, from raw sequences to phased haplotypes, batteries included. Works with WGS too!☆19Apr 22, 2026Updated last week
- ☆19May 27, 2022Updated 3 years ago
- A k-mer-based maximum likelihood method for estimating distances of reads to genomes and phylogenetic placement.☆23Mar 28, 2026Updated last month
- Reproducible Reporting with R (R3) training materials for marine ecosystem indicators☆13Sep 7, 2021Updated 4 years ago
- Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.☆89Apr 13, 2026Updated 2 weeks ago
- Tutorials on phylogenetic and phylogenomic inference☆51May 4, 2025Updated 11 months ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Modification of BayesAss 3.0.4 to allow handling of large SNP datasets☆17Feb 19, 2022Updated 4 years ago
- Scripts and resources for the haploblocks manuscript☆18Mar 20, 2020Updated 6 years ago
- Various scripts that I have created that are useful for genome annotation (repeats & proteins)☆17Feb 21, 2022Updated 4 years ago
- A guide to manipulating genotypic data across the common formats: VCF, EIGENSTRAT and PLINK (PACKEDPED) files. Includes how to convert be…☆24Aug 9, 2023Updated 2 years ago
- Quantifying Introgression via Branch Lengths☆57Sep 30, 2022Updated 3 years ago
- Framework for analyzing low depth NGS data in heterogeneous populations using PCA.☆61Jun 27, 2025Updated 10 months ago
- Random scripts, mostly for dealing with RADseq data and DNA sequence alignments☆18Oct 2, 2025Updated 6 months ago
- Compute various quantitative genetics parameters from a Generalised Linear Mixed Model (GLMM) estimates. Especially, it yields the observ…☆16Jan 20, 2025Updated last year
- Population Assignment using Genetic, Non-genetic or Integrated Data in a Machine-learning Framework. Methods in Ecology and Evolution.…☆16Sep 12, 2025Updated 7 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- An open-source data management system for tracking environmental DNA samples and metadata☆15Aug 8, 2024Updated last year
- An Efficient Swiss Army Knife for Population Genomic Analyses in R☆39May 21, 2024Updated last year
- ☆15Dec 7, 2023Updated 2 years ago
- metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.☆18Jul 31, 2025Updated 8 months ago
- Template repository for standardizing thematic species checklist data to Darwin Core using R☆18Mar 20, 2026Updated last month
- Detecting cancer subtypes with machine learning.☆10Feb 5, 2020Updated 6 years ago
- Copy number variation detection using NGS data.☆21Oct 26, 2023Updated 2 years ago