Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described in the Bioinformatics journal paper (2020) by Firtina et al. at https://people.inf.ethz.ch/omutlu/pub/apollo-technology-independent-genome-asse…
☆28May 10, 2020Updated 6 years ago
Alternatives and similar repositories for Apollo
Users that are interested in Apollo are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- AirLift is a tool that updates mapped reads from one reference genome to another. Unlike existing tools, It accounts for regions not shar…☆28May 23, 2024Updated 2 years ago
- FastRemap, a C++ tool for quickly remapping reads between genome assemblies based on the commonly used CrossMap tool. Link to paper: http…☆26Aug 24, 2022Updated 4 years ago
- The shiny app that accompanies the ngsReports R package☆14Jun 10, 2021Updated 5 years ago
- Peregrine: Fast Genome Assembler Using SHIMMER Index☆102Feb 6, 2022Updated 4 years ago
- An accurate and ultra-fast hybrid genome assembler☆88Apr 10, 2024Updated 2 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- A nextflow pipeline for polishing CLR assemblies☆18Feb 3, 2023Updated 3 years ago
- Shouji is fast and accurate pre-alignment filter for banded sequence alignment calculation. Described in the Bioinformatics journal paper…☆19Jun 3, 2019Updated 7 years ago
- ApHMM-GPU is the first GPU implementation of the Baum-Welch algorithm for profile Hidden Markov Models (pHMMs). It includes many of the s…☆11Jul 21, 2022Updated 4 years ago
- Long read aligner☆115May 26, 2023Updated 3 years ago
- SneakySnake is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU arch…☆57Mar 31, 2023Updated 3 years ago
- A filter algorithm with program to filter an alignment or mapping file☆13May 15, 2025Updated last year
- A simple-to-use tool for visualizing and comparing genome contexts for numerous genomes☆18Dec 1, 2025Updated 11 months ago
- Chromosome-level scaffolding using multiple references☆170Sep 8, 2024Updated 2 years ago
- Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metag…☆19Sep 4, 2024Updated 2 years 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.
- abPOA: an SIMD-based C library for fast partial order alignment using adaptive band☆148Sep 17, 2026Updated last month
- BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper☆53May 16, 2022Updated 4 years ago
- Source code of the processing-in-memory simulator used in the GRIM-Filter paper published at BMC Genomics in 2018: "GRIM-Filter: Fast See…☆11Feb 5, 2018Updated 8 years ago
- A tool for visualisation of gene set over-representation analysis (GSOA).☆10Jun 27, 2019Updated 7 years ago
- BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy…☆47May 10, 2023Updated 3 years ago
- Parallel String Graph Construction, Transitive Reduction, and Contig Generation for De Novo Genome Assembly☆16Jun 11, 2024Updated 2 years ago
- A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.☆213Nov 18, 2022Updated 3 years ago
- BOSTIn is a new, user-friendly phylogenetic artifact identification package.☆13Jul 11, 2026Updated 3 months ago
- Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.☆26Oct 24, 2025Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- uorf4u is a bioinformatics tool for conserved upstream ORF annotation.☆16Sep 16, 2025Updated last year
- Assembler for raw de novo genome assembly of long uncorrected reads.☆35Dec 11, 2019Updated 6 years ago
- Alignment-Free methods Adjusted by Neural Network☆13Feb 20, 2020Updated 6 years ago
- Annotation Extraction Genomic Integration Suite (AEGIS) is a powerful and flexible Python-based suite for the manipulation, analysis, and…☆15Updated this week
- an ensemble usage of MAFFT-linsi --add on large datasets☆13May 31, 2024Updated 2 years ago
- Source code for the software implementations of the GenASM algorithms proposed in our MICRO 2020 paper: Senol Cali et. al., "GenASM: A Hi…☆32Dec 19, 2022Updated 3 years ago
- ☆46Apr 18, 2026Updated 6 months ago
- run-length BWT tools for genomic sequences☆18May 19, 2022Updated 4 years ago
- 🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs☆67Aug 28, 2026Updated 2 months ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- just annotate it, dammit!☆94Aug 22, 2023Updated 3 years ago
- finshingTool☆54Nov 22, 2016Updated 9 years ago
- K-mer counting algorithms and count-data utilities for the BioJulia framework☆11Apr 23, 2023Updated 3 years ago
- Find, circularise and annotate mitogenome from PacBio assemblies☆204May 11, 2025Updated last year
- amplicon/smMIP mapping and analysis pipeline☆11Dec 8, 2022Updated 3 years ago
- a broadly applicable tool for automated gene identification and retrieval☆42Jun 16, 2026Updated 4 months ago
- MarginPolish: Graph based assembly polishing☆48Nov 24, 2020Updated 5 years ago