Quickly calculate and visualize sequence coverage in alignment files
☆101Jun 22, 2019Updated 7 years ago
Alternatives and similar repositories for bamcov
Users that are interested in bamcov are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Somatic (mosaic) SNV caller for 10X Genomics data using random forest classification and feature-based filters☆23Apr 1, 2019Updated 7 years ago
- PanEffect is a JavaScript framework to explore variant effects across a pangenome. The tool has two views that allows a user to (1) expl…☆13Jan 30, 2024Updated 2 years ago
- Genome inference from a population reference graph☆96Apr 1, 2025Updated last year
- Collection of simple C scripts for parsing vcf or bam files using the htslib C library. These scripts can be used as the starting point f…☆11Dec 11, 2020Updated 5 years ago
- A read extraction and realignment tool for next generation sequencing data☆107Oct 29, 2022Updated 3 years ago
- 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.
- Pan-genome inference and genotyping with long noisy or short accurate reads☆119Dec 13, 2024Updated last year
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆145Aug 24, 2025Updated 11 months ago
- Accurate and fast taxonomic classification using pseudoaligning☆21Sep 16, 2017Updated 8 years ago
- Peregrine: Fast Genome Assembler Using SHIMMER Index☆102Feb 6, 2022Updated 4 years ago
- An efficient index for the colored, compacted, de Bruijn graph☆112Jun 19, 2026Updated last month
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 3 years ago
- Bonsai: Fast, flexible taxonomic analysis and classification☆70Apr 9, 2024Updated 2 years ago
- The next version of bwa-mem☆857Oct 15, 2025Updated 10 months ago
- Efficient C functions to compute the summary statistics (flagstats) for sequencing read sets.☆15Aug 1, 2026Updated 2 weeks 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.
- SRF: Satellite Repeat Finder☆108Jan 8, 2024Updated 2 years ago
- a toolset for efficient analysis of 10X Genomics linked read data sets, in particular for de novo assembly☆15Nov 27, 2019Updated 6 years ago
- A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region exp…☆28Jun 25, 2026Updated last month
- BigWig and BAM utilities☆103Mar 26, 2024Updated 2 years ago
- Detection and genotyping of structural variants☆22May 27, 2026Updated 2 months ago
- Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly☆531Sep 27, 2023Updated 2 years ago
- An Artificial Neural Network-based discriminator for validating clinically significant genomic variants☆35Dec 25, 2023Updated 2 years ago
- Implicit Interval Tree with Interpolation Index☆43Jul 13, 2022Updated 4 years ago
- Plot structural variant signals from many BAMs and CRAMs☆572Jul 13, 2024Updated 2 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- genotyping by Mapping-free ALternate-allele detection of known VAriants☆10Mar 6, 2023Updated 3 years ago
- simple and not slow ORF caller☆24Apr 7, 2026Updated 4 months ago
- ☆290Dec 29, 2025Updated 7 months ago
- Genome browser and variant annotation☆397Jun 25, 2026Updated last month
- Simulate mutations in genomes☆15Jun 15, 2020Updated 6 years ago
- Toolkit for calling structural variants using short or long reads☆115Jul 14, 2026Updated last month
- Long read aligner☆115May 26, 2023Updated 3 years ago
- Highly sensitive pathogen detection☆12Oct 5, 2020Updated 5 years ago
- ✏️ Genome assembly polishing & SNV detection☆74Jun 12, 2026Updated 2 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- FlowCraft: a component-based pipeline composer for omics analysis using Nextflow.☆251Aug 10, 2025Updated last year
- Raspir, the rare species identifier☆11Oct 19, 2023Updated 2 years ago
- De novo genome assembler.☆12Jul 30, 2018Updated 8 years ago
- reference free variant assembly☆34Jul 14, 2023Updated 3 years ago
- don't get DUP'ed or DEL'ed by your putative SVs.☆109Dec 14, 2020Updated 5 years ago
- Experiments for "Scaling read aligners to hundreds of threads on general-purpose processors"☆11Jun 8, 2018Updated 8 years ago
- A web-based, interactive pangenome visualization tool☆21Apr 10, 2023Updated 3 years ago