imgag / ngs-bits

*ngs-bits* - Short-read and long-read sequencing tools for diagnostics Installation Binaries of *ngs-bits* are available via Bioconda: • **Binaries** for Linux/macOS Alternatively, *ngs-bits* can be built from sources. Use git to clone the most recent release (the source code package of GitHub does not contains required sub-modules): > git clone --recursive https://github.com/imgag/ngs-bits.git > cd ngs-bits > git checkout 2025_12 > git submodule update --recursive --init Depending on your operating system, building instructions vary slightly: • Building from **sources** for Linux • Building from **sources** for MacOS • Building from **sources** for Windows app requires a running server, instructions on how to deplpy it on a Linux machine can be found here Support Please report any issues or questions to the ngs-bits issue tracker. Documentation The documentation of individual tools is linked in the tools list below. For some tools the documentation pages contain only the command-line help, for other tools they contain more information. If you want to contribute, check the development documentation. License *ngs-bits* is provided under the MIT license, but is is based on other software components with different lincenses: • Qt is our base framwork for the graphical user interface, platform abstraction, data structures and much more. • htslib for HTS data format support (BAM, VCF, ...) • SimpleCrypt for weak encryption • QR-Code-generator for QR code generation ChangeLog Change log is available on the releases page. Citing You can cite ngs-bits in using Zenodo DOIs: • 2025_12: • 2025_09: A list of all releases/DOIs can be found here. Tools list _ngs-bits_ contains a lot of tools that are used for NGS-based diagnostics in our institute. Some of the tools need the NGSD, a database that contains for example gene, transcript and exon data. Installation instructions for the NGSD can be found here. Main tools • SeqPurge - A highly-sensitive adapter trimmer for paired-end short-read data. • SampleSimilarity - Calculates pairwise sample similarity metrics from VCF/BAM files. • SampleIdentity - Tries to identify datasets that are from the same patient based on BAM/CRAM files of WGS/WES/lrGS/RNA sequencing. • SampleGender - Determines sample gender based on a BAM file. • SampleAncestry - Estimates the ancestry of a sample based on variants. • CnvHunter - CNV detection from targeted resequencing data using non-matched control samples. • RohHunter - ROH detection based on a variant list annotated with AF values. • UpdHunter - UPD detection from trio variant data. QC tools The default output format of the quality control tools is qcML, an XML-based format for -omics quality control, that consists of an XML schema, which defined the overall structure of the format, and an ontology which defines the QC metrics that can be used. • ReadQC - Quality control tool for FASTQ files. • MappingQC - Quality control tool for a BAM file. • VariantQC - Quality control tool for a VCF file. • SomaticQC - Quality control tool for tumor-normal pairs (paper). • TrioMaternalContamination - Detects maternal contamination of a child using SNPs from parents. • TrioMendelianErrors - Determines mendelian error rate form a trio VCF file. • RnaQC - Calculates QC metrics for RNA samples. • QcToTsv - Converts qcML files to a TSV file. BAM tools • BamClipOverlap - (Soft-)Clips paired-end reads that overlap. • BamDownsample - Downsamples a BAM file to the given percentage of reads. • BamExtract - Extract reads from BAM/CRAM by read name. • BamFilter - Filters a BAM file by multiple criteria. • BamHighCoverage - Determines high-coverage regions in a BAM file. • BamInfo - Basic BAM information. • BamToFastq - Converts a coordinate-sorted BAM file to FASTQ files. • FastaFromBam - Download the reference genome FASTA file for a BAM/CRAM file. BED tools • BedAdd - Merges regions from several BED files. • BedAnnotateFromBed - Annotates BED file regions with information from a second BED file. • BedAnnotateGC - Annnotates the regions in a BED file with GC content. • BedAnnotateGenes - Annotates BED file regions with gene names (needs NGSD). • BedChunk - Splits regions in a BED file to chunks of a desired size. • BedCoverage - Annotates the regions in a BED file with the average coverage in one or several BAM files. • BedExtend - Extends the regions in a BED file by _n_ bases. • BedGeneOverlap - Calculates how much of each overlapping gene is covered (needs NGSD). • BedHighCoverage - Detects high-coverage regions from a BAM file. • BedInfo - Prints summary information about a BED file. • BedIntersect - Intersects two BED files. • BedLiftOver - Lift-over of regions in a BED file to a different genome build. • BedLowCoverage - Calcualtes regions of low coverage based on a input BED and BAM file. • BedMerge - Merges overlapping regions in a BED file. • BedReadCount - Annoates the regions in a BED file with the read count from a BAM file. • BedShrink - Shrinks the regions in a BED file by _n_ bases. • BedSort - Sorts the regions in a BED file • BedSubtract - Subracts one BED file from another BED file. • BedToFasta - Converts BED file to a FASTA file (based on the reference genome). • CnvReferenceCohort - Create a reference cohort for CNV calling from a list of coverage profiles. FASTQ tools • FastqAddBarcode - Adds sequences from separate FASTQ as barcodes to read IDs. • FastqConvert - Converts the quality scores from Illumina 1.5 offset to Sanger/Illumina 1.8 offset. • FastqConcat - Concatinates several FASTQ files into one output FASTQ file. • FastqDownsample - Downsamples paired-end FASTQ files. • FastqExtract - Extracts reads from a FASTQ file according to an ID list. • FastqExtractBarcode - Moves molecular barcodes of reads to a separate file. • FastqExtractUMI - Moves unique moleculare identifier from read sequence to read ID. • FastqFormat - Determines the quality score offset of a FASTQ file. • FastqList…