pughlab / ConsensusCruncher
ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to amalgamate reads derived from the same DNA template into a consensus sequence.
☆21Updated 2 years ago
Alternatives and similar repositories for ConsensusCruncher:
Users that are interested in ConsensusCruncher are comparing it to the libraries listed below
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA☆27Updated 4 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆29Updated 6 years ago
- Microsatellite instability (MSI) detection for cfDNA samples.☆19Updated 4 years ago
- SMN1 copy-number and sequence variant analysis from next generation sequencing data☆22Updated last year
- Tools for processing and analyzing structural variants.☆33Updated 9 years ago
- Scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods☆46Updated 2 years ago
- A simplified pipeline for ctDNA sequencing data analysis☆36Updated 7 years ago
- Python scripts for matching output of Pacific Biosciences IsoSeq RNA-seq pipeline to an annotation file.☆23Updated 9 years ago
- ☆46Updated 5 years ago
- High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants☆22Updated 5 years ago
- ONCOCNV - a package to detect copy number changes in Targeted Deep Sequencing and Exome-seq data☆25Updated 2 years ago
- QDNAseq package for Bioconductor☆49Updated 8 months ago
- smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very…☆20Updated 5 years ago
- ☆53Updated 2 years ago
- A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…☆31Updated 3 years ago
- WISECONDOR (WIthin-SamplE COpy Number aberration DetectOR): Detect fetal trisomies and smaller CNV's in a maternal plasma sample using wh…☆44Updated 11 months ago
- Full-spectrum copy number variation detection by high-throughput DNA sequencing☆37Updated 3 years ago
- R package for inferring copy number from read depth☆32Updated 2 years ago
- heuristics to merge structural variant calls in VCF format.☆36Updated 8 years ago
- SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …☆42Updated this week
- QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.☆32Updated 8 years ago
- Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses☆31Updated 3 years ago
- CN-Learn☆29Updated 5 years ago
- CNV screening and annotation tool☆24Updated 8 years ago
- Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)☆41Updated 10 months ago
- This repo is be archived, these workflows are still housed housed in the GATK repository under the scripts directory. The workflows are a…☆21Updated 5 years ago
- Remove primer sequence from BAM alignments by soft-clipping☆31Updated 5 years ago
- For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and…☆35Updated last year
- Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of func…☆27Updated last year
- Preprocessing tools for unique molecular index (UMI) sequencing reads☆31Updated last year