microsatellite instability detection using tumor only or paired tumor-normal data
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Updated
Jan 6, 2021 - C++
microsatellite instability detection using tumor only or paired tumor-normal data
AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.
Sequence alignment tools
Process Illumina instrument data into SAM/BAM/CRAM files.
Multi-sample somatic variant caller
Parse and process SAM and BAM formatted files
vSNP -- validate SNPs
📇 Retrieve data in genomic intervals with a Python interface for tabix.
Splice junction analysis and filtering from BAM files
🚦 Run Picard on BAM files and collate 90 metrics into one file.
Ribo-seq TIS Hunter, predicting translation initiation sites and ORFs using riboseq data
The DKFZ alignment workflow plugin originally developed at the eilslabs
Genome browser and variant annotation
Datastores for reads, not your papa's FASTQ files.
Utilities for analyzing next generation sequencing data.
Nextflow-based BAM-to-FASTQ conversion and FASTQ-sorting workflow.
⛰ covtobed | Convert the coverage track from a BAM file into a BED file
knowledge-based genotyping of cancer hotspots from the tumor BAM files
Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.
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