sudmantlab / loco-pipeView external linksLinks
loco-pipe is an automated Snakemake pipeline that streamlines a set of essential population genomic analyses for low-coverage whole genome sequencing (lcWGS) data
☆29Jan 21, 2026Updated 3 weeks ago
Alternatives and similar repositories for loco-pipe
Users that are interested in loco-pipe are comparing it to the libraries listed below
Sorting:
- Bioinformatics pipeline to process whole genome resequencing data and perform genotype likelihood based population genomic analyses using…☆26Jan 12, 2026Updated last month
- Scripts for going from raw .fastq files to processed and quality-checked .bam files for downstream analysis☆14Nov 23, 2021Updated 4 years ago
- Pipeline for GTseq genotyping and quality control☆15Jan 30, 2023Updated 3 years ago
- Copy number variation detection using NGS data.☆19Oct 26, 2023Updated 2 years ago
- CCB Skills Seminar (Fall 2023) - snakemake☆19Oct 16, 2023Updated 2 years ago
- Trim, Align to genome, Deduplicate, Realign WGS sequencing samples☆17Feb 4, 2026Updated last week
- A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - fo…☆112Jun 24, 2025Updated 7 months ago
- Scripts used to perform analyses in Rice et al. (2023)☆16Dec 28, 2023Updated 2 years ago
- Framework for analyzing low depth NGS data in heterogeneous populations using PCA.☆58Jun 27, 2025Updated 7 months ago
- ☆103Oct 14, 2021Updated 4 years ago
- CLfinder-OrthNet, a pipeline to encode orthologs from multiple genomes and their evolutionary history into networks (OrthNets) based on c…☆10Jun 9, 2022Updated 3 years ago
- ☆12Jun 12, 2023Updated 2 years ago
- An R package to identify and classify duplicated genes from whole-genome protein sequence data☆31Sep 11, 2025Updated 5 months ago
- WinPCA. A package for windowed principal component analysis.☆45Feb 2, 2026Updated last week
- Files for the the Physalia course on Population genomic inference from low-coverage whole-genome sequencing data, Oct 10-13, 2022☆69Oct 24, 2025Updated 3 months ago
- 🚝RAILS and 👞🔨Cobbler: Assembly Improvement by Long Sequence Scaffolding/Gap-filling☆27Jan 2, 2024Updated 2 years ago
- Synteny matrix representation with maximum likelihood pipeline☆16Jul 7, 2021Updated 4 years ago
- Process linked-read data, from raw sequences to phased haplotypes, batteries included. Works with WGS too!☆18Feb 6, 2026Updated last week
- Set of script for the paper on the cattle graph genome☆13Jan 10, 2023Updated 3 years ago
- A k-mer-based maximum likelihood method for estimating distances of reads to genomes and phylogenetic placement.☆18Feb 6, 2026Updated last week
- Pipelines for analyzing genomic or transcriptomic data☆17Feb 29, 2024Updated last year
- A loose collection of scripts and utilities for processing and analyzing the Goat reference genome assembly☆11Feb 28, 2017Updated 8 years ago
- An Efficient Swiss Army Knife for Population Genomic Analyses in R☆38May 21, 2024Updated last year
- Analysis of gene expression and splicing diversity in a subset of samples from the 1000 Genomes Project, including eQTL and sQTL discover…☆42Jul 19, 2024Updated last year
- Code for assembly approach presented in "Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspri…☆14Nov 20, 2023Updated 2 years ago
- mtGrasp: de novo reference-grade mitochondrial genome assembly and standardization☆24Feb 3, 2026Updated last week
- Estimation of per-individual inbreeding tracts under a probabilistic framework☆15Aug 11, 2023Updated 2 years ago
- Leroy & Rougemont - “learning-by-doing” introduction to population genomics - scripts☆21Oct 2, 2019Updated 6 years ago
- A pipeline for phasing UK Biobank whole genome sequence data☆19Mar 21, 2023Updated 2 years ago
- ☆16Apr 9, 2021Updated 4 years ago
- Software package for estimating fine-scale recombination rate.☆17Jun 8, 2021Updated 4 years ago
- visualization of phylogenetic output files☆14Oct 23, 2023Updated 2 years ago
- Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome☆86Jan 28, 2026Updated 2 weeks ago
- Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files, rename fasta files (prefix a…☆22Oct 21, 2025Updated 3 months ago
- The Vertebrate Genomes Project Mitogenome Assembly Pipeline☆19Mar 26, 2023Updated 2 years ago
- GWAS QC, PCA, haplotype phasing, genotype imputation☆20Aug 13, 2025Updated 6 months ago
- scripts for the project of seven thaliana genomes assembly☆42May 22, 2021Updated 4 years ago
- ☆21Oct 2, 2024Updated last year
- ☆18Dec 15, 2021Updated 4 years ago