DKFZ OTP Pipelines

Trim Galore — convenience wrapper around Cutadapt and FastQC for consistent, automated adapter trimming, quality filtering, and post-trimming QC of high-throughput sequencing reads. Auto-detects Illum

3 shared topics • 2 shared operations

Novocraft suite — short-read alignment and BAM sorting for DNA-seq and RNA-seq. novoalign maps Illumina, Ion Torrent, and 454 reads to indexed reference genomes with Smith-Waterman scoring for high-ac

3 shared topics • 1 shared operation

cellSNP-lite — fast C-based tool for genotyping single cells and bulk samples at known or de-novo SNP sites from BAM/SAM files. Generates sparse genotype matrices (AD/DP/OTH counts) in VCF/BCF format

2 shared topics • 2 shared operations

iClusterPlus — Bioconductor R package for integrative clustering of multi-omics data. Performs joint latent variable modeling of multiple genomic data types (e.g., SNP copy number, methylation, gene e

2 shared topics • 2 shared operations

Use when working with nf-core/rnafusion — a Nextflow pipeline for RNA fusion gene detection and quantification. Detects fusion transcripts from RNA-seq data using up to six callers (STAR-Fusion, Arrib

2 shared topics • 2 shared operations