SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
☆42Apr 7, 2022Updated 3 years ago
Alternatives and similar repositories for squid
Users that are interested in squid are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆14Aug 30, 2025Updated 6 months ago
- VariantStore: A Large-Scale Genomic Variant Search Index☆39Jul 9, 2021Updated 4 years ago
- Scallop is a reference-based transcriptome assembler for RNA-seq☆92Apr 30, 2021Updated 4 years ago
- Fast fusion detection using kallisto☆79Jun 11, 2025Updated 9 months ago
- Prepare Sailfish and Salmon output for downstream analysis☆42Jun 6, 2019Updated 6 years ago
- Hidden Markov Model based Copy number caller☆20Dec 9, 2025Updated 3 months ago
- ☆14May 12, 2023Updated 2 years ago
- Ximmer is a system for CNV calling on exome and targeted genomic sequencing☆19Jan 28, 2026Updated last month
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Jun 7, 2019Updated 6 years ago
- a pileup library that embraces the huge☆43Oct 2, 2020Updated 5 years ago
- Visualisation and prioritisation of genomic variants from human exome sequencing projects☆13Apr 23, 2019Updated 6 years ago
- An efficient index for the colored, compacted, de Bruijn graph☆111Mar 11, 2026Updated 2 weeks ago
- Toolkit for automated and rapid discovery of structural variants☆24Aug 24, 2023Updated 2 years ago
- RNA-seq analysis pipeline for detection of gene-fusions☆172Updated this week
- MEM mapper prototype☆13Nov 28, 2020Updated 5 years ago
- Learn tissue-specificity and tissue-sharing of genetic regulation across 49 tissues using constraint matrix factorization model☆22Oct 9, 2020Updated 5 years ago
- Mutation rate analysis of autosomal loci☆15Jun 25, 2020Updated 5 years ago
- Add functional variant annotation to MAF file☆11Nov 20, 2024Updated last year
- ☆73Mar 1, 2019Updated 7 years ago
- k-mer similarity analysis pipeline☆22Nov 20, 2025Updated 4 months ago
- Dynamic programming for aa-to-nt alignment with affine gap, splicing and frameshift☆19Sep 30, 2024Updated last year
- A read extraction and realignment tool for next generation sequencing data☆106Oct 29, 2022Updated 3 years ago
- SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations o…☆119Feb 8, 2026Updated last month
- fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"☆306Nov 14, 2025Updated 4 months ago
- C++ library for analysing and storing large-scale cohorts of sequence variant data☆17Aug 27, 2019Updated 6 years ago
- Probabilistic HLA typing☆35Aug 31, 2019Updated 6 years ago
- A Julia package for extracting mutation signatures using topic models☆19Feb 23, 2022Updated 4 years ago
- ☆12Apr 16, 2021Updated 4 years ago
- genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF☆148Feb 17, 2026Updated last month
- Detecting sites of genomic enrichment☆199May 8, 2023Updated 2 years ago
- Microassembly based somatic variant caller for NGS data☆154Jun 23, 2022Updated 3 years ago
- toolkit to process gtf files☆17Dec 24, 2021Updated 4 years ago
- Code for performing PCA followed by CCA☆18Dec 2, 2018Updated 7 years ago
- An R package to time somatic mutations☆67Dec 12, 2020Updated 5 years ago
- Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …☆231Jun 1, 2024Updated last year
- Fast and accurate gene fusion detection from RNA-Seq data☆262Sep 21, 2025Updated 6 months ago
- Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long read…☆12Jan 22, 2020Updated 6 years ago
- Whole genome workflows☆13Nov 9, 2024Updated last year
- seqcover allows users to view coverage for hundreds of genes and dozens of samples☆51Apr 9, 2021Updated 4 years ago