HuntsmanCancerInstitute / USeqLinks
180+ Java applications for analyzing next generation sequencing data from ChIPSeq, RNASeq, BisSeq, DNASeq, variant annotation/ filtering, alignment/VCF QC, capture array design, IGV/ DAS2/IGB/UCSC file manipulation, etc. Both GUI and cmd line interfaces.
☆18Updated 2 weeks ago
Alternatives and similar repositories for USeq
Users that are interested in USeq are comparing it to the libraries listed below
Sorting:
- for visual evaluation of read support for structural variation☆54Updated last year
- Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer☆47Updated this week
- Gene Fusion Visualiser☆51Updated 2 years ago
- novoBreak: local assembly for breakpoint detection in cancer genomes☆26Updated 7 years ago
- Full-spectrum copy number variation detection by high-throughput DNA sequencing☆37Updated 3 years ago
- Splice junction analysis and filtering from BAM files☆40Updated 3 years ago
- CAVA (Clinical Annotation of VAriants)☆14Updated 6 years ago
- A python package and a set of shell commands to handle GTF files☆49Updated last year
- smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very…☆20Updated 6 years ago
- ⛏ HLA predictions from NGS shotgun data☆53Updated last month
- A Framework to call Structural Variants from NGS based datasets☆22Updated 7 years ago
- ☆51Updated 5 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆29Updated 7 years ago
- RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference…☆67Updated 2 years ago
- ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…☆22Updated 2 years ago
- Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…☆45Updated 2 years ago
- Long read to rMATS☆31Updated 2 years ago
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA☆27Updated 4 years ago
- Useful tools for working with Salmon output☆38Updated 5 years ago
- Structural variant VCF annotation, duplicate removal and comparison☆33Updated 4 months ago
- ONCOCNV - a package to detect copy number changes in Targeted Deep Sequencing and Exome-seq data☆25Updated 2 years ago
- Opossum is a tool to pre-process RNA-seq reads prior to variant calling.☆28Updated 7 years ago
- A set of tools to annotate VCF files with expression and readcount data☆29Updated 4 months ago
- Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)☆41Updated last year
- For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and…☆35Updated 2 years ago
- MetaSV: An accurate and integrative structural-variant caller for next generation sequencing☆56Updated 8 years ago
- Calib clusters barcode tagged paired-end reads based on their barcode and sequence similarity.☆39Updated 2 years ago
- A bioinformatics tool for SV detection and virus integration discovery☆20Updated 7 years ago
- Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA☆29Updated last year
- Simplify snpEff annotations for interesting cases☆22Updated 6 years ago