gt1 / biobambam2View external linksLinks
Tools for early stage alignment file processing
☆95Mar 12, 2019Updated 6 years ago
Alternatives and similar repositories for biobambam2
Users that are interested in biobambam2 are comparing it to the libraries listed below
Sorting:
- Tools for bam file processing☆55Apr 20, 2015Updated 10 years ago
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆238Aug 11, 2021Updated 4 years ago
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 years ago
- Tools for next-generation sequencing analysis☆89Jun 25, 2019Updated 6 years ago
- Tools for working with SAM/BAM data☆605Dec 22, 2024Updated last year
- annotate a VCF with other VCFs/BEDs/tabixed files☆396Aug 30, 2025Updated 5 months ago
- Fast fusion detection using kallisto☆79Jun 11, 2025Updated 8 months ago
- VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.☆99May 21, 2024Updated last year
- goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary☆224Sep 18, 2025Updated 4 months ago
- A tool set for short variant discovery in genetic sequence data.☆204May 4, 2021Updated 4 years ago
- ☆92Jan 11, 2022Updated 4 years ago
- Rapid sensitive and accurate read mapping via quasi-mapping☆90Jun 5, 2020Updated 5 years ago
- adds sample names and read-group (RG) tags to BAM alignments☆51Dec 14, 2020Updated 5 years ago
- Integrated toolkit for analysis and evaluation of annotated genomes☆25Aug 1, 2025Updated 6 months ago
- Create Bloom filters for a given reference and then use it to categorize sequences☆76Nov 26, 2024Updated last year
- RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.☆14Nov 10, 2025Updated 3 months ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆331May 27, 2025Updated 8 months 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
- Smart VCF parser DSL☆83May 24, 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
- C++ API & command-line toolkit for working with BAM data☆429May 18, 2025Updated 8 months ago
- BAM Statistics, Feature Counting and Annotation☆152Updated this week
- Count bases in BAM/CRAM files☆323Jan 31, 2022Updated 4 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
- Microassembly based somatic variant caller for NGS data☆154Jun 23, 2022Updated 3 years ago
- a lightweight db framework for exploring genetic variation.☆324Apr 28, 2020Updated 5 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
- iAnnotateSV is a Python library and command-line software toolkit to annotate and visualize structural variants detected from Next Genera…☆16Dec 31, 2025Updated last month
- de Bruijn Graph REAd mapping Tool☆14Jul 12, 2017Updated 8 years ago
- ☆12Jan 21, 2016Updated 10 years ago
- lumpy: a general probabilistic framework for structural variant discovery☆337Jun 7, 2022Updated 3 years ago
- a wee tool for random access into BGZF files.☆86May 10, 2018Updated 7 years ago
- Concordance and contamination estimator for tumor–normal pairs☆59Oct 22, 2024Updated last year
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,026Aug 24, 2024Updated last year
- collection of data structures and algorithms☆19Mar 19, 2019Updated 6 years ago
- A read extraction and realignment tool for next generation sequencing data☆104Oct 29, 2022Updated 3 years ago
- MetaSV: An accurate and integrative structural-variant caller for next generation sequencing☆59Jun 30, 2017Updated 8 years ago
- for visual evaluation of read support for structural variation☆56Jun 4, 2024Updated last year
- DeeNA Zip (SAM/BAM compression tool)☆13May 25, 2019Updated 6 years ago