patidarr / ngs_pipeline
Exome/Capture/RNASeq Pipeline Implementation using snakemake
☆45Updated 6 years ago
Related projects ⓘ
Alternatives and complementary repositories for ngs_pipeline
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆50Updated 4 years ago
- ☆78Updated 10 years ago
- ☆65Updated last year
- Documenting usage and experience with bioinformatic tools☆40Updated 9 years ago
- tools to find circRNAs in RNA-seq data☆40Updated 7 years ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆94Updated 3 years ago
- 10x Genomics Linked-Read Diploid De Novo Assembler☆64Updated 5 years ago
- ☆38Updated 9 months ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- ☆37Updated last year
- csf fork of fastqc for usage on selected reads of unaligned bam file☆49Updated 11 years ago
- Burden testing against public controls☆50Updated 8 months ago
- A software for calculating telomere length☆67Updated 6 years ago
- RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.☆36Updated 2 years ago
- QDNAseq package for Bioconductor☆48Updated 3 months ago
- Snakemake based pipeline for RNA-Seq analysis☆31Updated 5 years ago
- identifying mutational significance in cancer genomes☆60Updated 2 years ago
- For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and…☆33Updated last year
- ☆53Updated 3 years ago
- DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies …☆36Updated 2 years ago
- Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data☆66Updated 2 months ago
- R package designed to simplify structural variant analysis☆70Updated 2 years ago
- Relevant papers for CNV and SV approaches☆94Updated 2 weeks ago
- Benchmarking of aligners and variant callers for Whole Exome Sequencing data☆19Updated 5 years ago
- CNV screening and annotation tool☆24Updated 8 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆28Updated 6 years ago
- ENCODE long read RNA-seq pipeline☆44Updated last year
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆96Updated 2 years ago
- Microsatellite instability (MSI) detection for tumor only data.☆94Updated 6 months ago