Tools for early stage alignment file processing
☆96Mar 12, 2019Updated 7 years ago
Alternatives and similar repositories for biobambam2
Users that are interested in biobambam2 are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Tools for bam file processing☆56Apr 20, 2015Updated 11 years ago
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆240Aug 11, 2021Updated 4 years ago
- Fast fusion detection using kallisto☆79Jun 11, 2025Updated 10 months ago
- A tool set for short variant discovery in genetic sequence data.☆205May 4, 2021Updated 5 years ago
- Tools for working with SAM/BAM data☆610Dec 22, 2024Updated last year
- 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.
- annotate a VCF with other VCFs/BEDs/tabixed files☆401May 1, 2026Updated last week
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 years ago
- collection of data structures and algorithms☆19Mar 19, 2019Updated 7 years ago
- goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary☆226Sep 18, 2025Updated 7 months ago
- VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.☆100Apr 19, 2026Updated 2 weeks ago
- Tools for next-generation sequencing analysis☆89Jun 25, 2019Updated 6 years ago
- ☆94Jan 11, 2022Updated 4 years ago
- adds sample names and read-group (RG) tags to BAM alignments☆51Dec 14, 2020Updated 5 years ago
- RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.☆14Nov 10, 2025Updated 5 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.
- a wee tool for random access into BGZF files.☆86May 10, 2018Updated 7 years ago
- Rapid sensitive and accurate read mapping via quasi-mapping☆90Jun 5, 2020Updated 5 years ago
- C++ API & command-line toolkit for working with BAM data☆429May 18, 2025Updated 11 months ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆335May 27, 2025Updated 11 months ago
- Create Bloom filters for a given reference and then use it to categorize sequences☆77Nov 26, 2024Updated last year
- ☆12Jan 21, 2016Updated 10 years ago
- Integrated toolkit for analysis and evaluation of annotated genomes☆25Aug 1, 2025Updated 9 months ago
- Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses☆31Feb 12, 2022Updated 4 years ago
- Smart VCF parser DSL☆83May 24, 2022Updated 3 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Minimal docker image for bwa. Not developed any more.☆11Apr 26, 2015Updated 11 years ago
- de Bruijn Graph REAd mapping Tool☆14Jul 12, 2017Updated 8 years ago
- Count bases in BAM/CRAM files☆324Jan 31, 2022Updated 4 years ago
- The BTL C/C++ Common bloom filters for bioinformatics projects, as well as any APIs created for other programming languages.☆18Feb 26, 2022Updated 4 years ago
- A flexible framework for rapid genome analysis and interpretation☆319Oct 18, 2022Updated 3 years ago
- To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be co…☆31Dec 26, 2023Updated 2 years ago
- Blast2Bam uses the XML results of Blastn, the reference and the fastQ or fasta file(s) to output a SAM file.☆49May 25, 2021Updated 4 years ago
- A tool to benchmark mappers and different parameters within minutes☆44Jul 2, 2019Updated 6 years ago
- BAM Statistics, Feature Counting and Annotation☆154Apr 16, 2026Updated 3 weeks ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- Microassembly based somatic variant caller for NGS data☆154Jun 23, 2022Updated 3 years ago
- SparkBWA is a new tool that exploits the capabilities of a Big Data technology as Apache Spark to boost the performance of one of the mos…☆69Sep 5, 2019Updated 6 years ago
- A read extraction and realignment tool for next generation sequencing data☆107Oct 29, 2022Updated 3 years ago
- Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.☆46Jan 18, 2019Updated 7 years ago
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,029Aug 24, 2024Updated last year
- MetaSV: An accurate and integrative structural-variant caller for next generation sequencing☆59Jun 30, 2017Updated 8 years ago
- Rapid Mapping-based Isoform Quantification from RNA-Seq Reads☆127Jun 9, 2022Updated 3 years ago