Spliced read mapper for RNA-Seq
☆92Jul 9, 2023Updated 2 years ago
Alternatives and similar repositories for tophat
Users that are interested in tophat are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆322Mar 31, 2020Updated 6 years ago
- Graph-based alignment (Hierarchical Graph FM index)☆540Jan 27, 2026Updated 4 months ago
- A fast and sensitive gapped read aligner☆795Jun 1, 2026Updated 2 weeks ago
- Rcount: simple and flexible RNA-Seq read counting☆12May 19, 2022Updated 4 years ago
- Near-optimal RNA-Seq quantification☆765Mar 16, 2026Updated 3 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆12Jan 21, 2016Updated 10 years ago
- FASTA/FASTQ pre-processing programs☆202Mar 4, 2022Updated 4 years ago
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆743Jun 8, 2026Updated last week
- A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.☆1,069Updated this week
- Gordon's Text utils Library☆10Apr 11, 2022Updated 4 years ago
- COMETgazer mehylation analysis software suite☆10Jul 21, 2019Updated 6 years ago
- BEDOPS: high-performance genomic feature operations☆369Apr 29, 2025Updated last year
- R function to plot high quality, elegant heatmap using 'ggplot2' graphics . Some of the important features of this package are, colorin…☆11Apr 19, 2016Updated 10 years ago
- An ultrafast memory-efficient short read aligner☆268May 11, 2022Updated 4 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Transcript assembly tool using multiple change-point inference to improve 3'UTR annotation☆13Dec 2, 2022Updated 3 years ago
- RNA-seq aligner☆2,208Mar 18, 2025Updated last year
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆471Apr 21, 2026Updated last month
- Cutadapt removes adapter sequences from sequencing reads☆582Jun 8, 2026Updated last week
- hs-blastn, a fast and accurate nucleotide-nucleotide sequences aligner.☆27Aug 12, 2020Updated 5 years ago
- R package for reading in & working with NucleoATAC outputs☆26Oct 13, 2018Updated 7 years ago
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,749Mar 22, 2025Updated last year
- Tools for bam file processing☆56Apr 20, 2015Updated 11 years ago
- A program for summarising CpG methylation patterns☆20Sep 9, 2016Updated 9 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.☆139Aug 21, 2024Updated last year
- Tools for next-generation sequencing analysis☆89Jun 25, 2019Updated 6 years ago
- Fast spliced aligner with low memory requirements☆40Sep 8, 2015Updated 10 years ago
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,914May 21, 2026Updated 3 weeks ago
- Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data☆214May 14, 2020Updated 6 years ago
- A flexible framework for rapid genome analysis and interpretation☆320Oct 18, 2022Updated 3 years ago
- Tool for stripping adaptors and/or merging paired reads with overlap into single reads.☆147Oct 4, 2016Updated 9 years ago
- Applying IDR analysis to Homer peaks.☆16May 8, 2020Updated 6 years ago
- Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data☆299Sep 6, 2025Updated 9 months 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.
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆241Aug 11, 2021Updated 4 years ago
- RNA-Skim: a rapid method for RNA-Seq quantification at transcript level☆19Sep 3, 2017Updated 8 years ago
- Spliced read mapper for RNA-Seq☆22May 24, 2018Updated 8 years ago
- Mostly deprecated in favor of : https://github.com/hbc/bcbioRNASeq. Quality control, differential gene/transcript expression and pathway …☆26Dec 11, 2017Updated 8 years ago
- A deletion finder through re-aligning the whole soft-clipping read☆12Jul 2, 2016Updated 9 years ago
- ☆97Sep 21, 2022Updated 3 years ago
- Strelka2 germline and somatic small variant caller☆394Apr 20, 2026Updated last month