Alternatives and similar repositories for grenepipe

Users that are interested in grenepipe are comparing it to the libraries listed below

• sudmantlab / loco-pipe

  View on GitHub
  loco-pipe is an automated Snakemake pipeline that streamlines a set of essential population genomic analyses for low-coverage whole genom…
  ☆29Jan 21, 2026Updated 3 weeks ago
• thecgs / quickprot

  View on GitHub
  QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics
  ☆16Jan 12, 2026Updated last month
• Gaius-Augustus / GUSHR

  View on GitHub
  Generating UTRs from SHort Reads
  ☆11Sep 28, 2020Updated 5 years ago
• lczech / grenedalf

  View on GitHub
  Toolkit for Population Genetic Statistics from Pool-Sequenced Samples, e.g., in Evolve and Resequence experiments
  ☆48Oct 15, 2025Updated 4 months ago
• WarrenLab / chicken-pangenome-paper

  View on GitHub
  Scripts used to perform analyses in Rice et al. (2023)
  ☆16Dec 28, 2023Updated 2 years ago
• dubssieg / pancat

  View on GitHub
  Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions
  ☆36May 14, 2025Updated 9 months ago
• schneebergerlab / AMPRIL-genomes

  View on GitHub
  scripts for the project of seven thaliana genomes assembly
  ☆42May 22, 2021Updated 4 years ago
• champost / ABLE

  View on GitHub
  ABLE - Approximate Blockwise Likelihood Estimation
  ☆17Jul 4, 2018Updated 7 years ago
• alshai / rowbowt

  View on GitHub
  run-length BWT tools for genomic sequences
  ☆19May 19, 2022Updated 3 years ago
• TBooker / PicMin

  View on GitHub
  ☆13Jun 6, 2023Updated 2 years ago
• petrelharp / local_pca

  View on GitHub
  Methods for examining PCA locally along the genome.
  ☆88Aug 13, 2024Updated last year
• kensung-lab / hypo

  View on GitHub
  HyPo: Super Fast & Accurate Polisher for Long Read Genome Assemblies
  ☆65Feb 23, 2020Updated 5 years ago
• DessimozLab / read2tree

  View on GitHub
  a tool for inferring species tree from sequencing reads
  ☆156Dec 9, 2025Updated 2 months ago
• EVidenceModeler / EVidenceModeler

  View on GitHub
  source code for EVM
  ☆122Nov 29, 2024Updated last year
• hillerlab / IterativeErrorCorrection

  View on GitHub
  Iterative error correction of long reads
  ☆13Dec 9, 2022Updated 3 years ago
• huangnengCSU / NanoSNP

  View on GitHub
  A deep learning-based SNP calling method to identify SNPs based on low-coverage Nanopore sequencing reads.
  ☆21Nov 20, 2022Updated 3 years ago
• hemstrow / snpR

  View on GitHub
  ☆31Jan 29, 2026Updated 2 weeks ago
• evotools / CattleGraphGenomePaper

  View on GitHub
  Set of script for the paper on the cattle graph genome
  ☆13Jan 10, 2023Updated 3 years ago
• pdimens / harpy

  View on GitHub
  Process linked-read data, from raw sequences to phased haplotypes, batteries included. Works with WGS too!
  ☆18Updated this week
• mossmatters / MJPythonNotebooks

  View on GitHub
  Visualizing gene tree conflict using Phyparts, and ETE3
  ☆14Jun 17, 2023Updated 2 years ago
• MaikeMorrison / FSTruct

  View on GitHub
  ☆13Aug 18, 2023Updated 2 years ago
• Gaius-Augustus / TSEBRA

  View on GitHub
  TSEBRA: Transcript Selector for BRAKER
  ☆49Nov 14, 2025Updated 3 months ago
• TobyBaril / EarlGrey

  View on GitHub
  Earl Grey: A fully automated TE curation and annotation pipeline
  ☆192Updated this week
• NESCent / MINOTAUR

  View on GitHub
  Multivariate vIsualisatioN and OuTlier Analysis Using R
  ☆14Apr 8, 2023Updated 2 years ago
• telatin / bamtocov

  View on GitHub
  🏔 coverage extraction from BAM/CRAM files, supporting targets 📊  
  ☆65Feb 2, 2026Updated 2 weeks ago
• sanger-pathogens / panito

  View on GitHub
  Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment
  ☆16Dec 5, 2018Updated 7 years ago
• Tom-Jenkins / utility_scripts

  View on GitHub
  Scripts for population genetics analysis
  ☆20Nov 10, 2022Updated 3 years ago
• NGSEP / NGSEPcore

  View on GitHub
  NGSEP is an integrated framework for analysis of short and long DNA high throughput sequencing reads. A complete list of functionalities …
  ☆57Updated this week
• harvardinformatics / snpArcher

  View on GitHub
  Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
  ☆87Feb 10, 2026Updated last week
• simonhmartin / genomics_general

  View on GitHub
  General tools for genomic analyses.
  ☆386Feb 28, 2025Updated 11 months ago
• huangnengCSU / compleasm

  View on GitHub
  A genome completeness evaluation tool based on miniprot
  ☆233Sep 18, 2025Updated 4 months ago
• alek0991 / iSAFE

  View on GitHub
  Pinpoints the mutation favored by selection
  ☆34Nov 2, 2021Updated 4 years ago
• tolkit / gfatk

  View on GitHub
  A plant organellar Graphical Fragment Assembly toolkit
  ☆16Sep 10, 2025Updated 5 months ago
• mbhall88 / skc

  View on GitHub
  Shared k-mer content between two genomes
  ☆19Jun 21, 2023Updated 2 years ago
• rebeccaserramari / polyploid-potato-assembly

  View on GitHub
  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
• vembrane / vembrane

  View on GitHub
  vembrane filters VCF records using python expressions
  ☆68Jan 8, 2026Updated last month
• jsevo / taxumap

  View on GitHub
  ☆16May 22, 2023Updated 2 years ago
• nt246 / lcwgs-guide-tutorial

  View on GitHub
  ☆103Oct 14, 2021Updated 4 years ago
• ctlab / GADMA

  View on GitHub
  Genetic Algorithm for Demographic Model Analysis
  ☆54Feb 3, 2026Updated 2 weeks ago