ngs-bits - Short-read sequencing tools

Obtaining ngs-bits

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 2024_06
> 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

Support

Please report any issues or questions to the ngs-bits issue tracker.

Documentation

Have a look at the ECCB'2018 poster.

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.

License

ngs-bits is provided under the MIT license and is based on other open source software:

• htslib for HTS data format support (BAM, VCF, ...)
• SimpleCrypt for weak encryption
• QR-Code-generator for QR code generation

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.
• 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 and example output data).
• TrioMaternalContamination - Detects maternal contamination of a child using SNPs from parents.
• RnaQC - Calculates QC metrics for RNA samples.

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.
• BamToFastq - Converts a coordinate-sorted BAM file to FASTQ files.

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).

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 - Lists read IDs and base counts.
• FastqMidParser - Counts the number of occurances of each MID/index/barcode in a FASTQ file.
• FastqToFasta - Converts FASTQ to FASTA format.
• FastqTrim - Trims start/end bases from the reads in a FASTQ file.

VCF tools (small variants)

• VcfAdd - Appends variants from a VCF file to another VCF file.
• VcfAnnotateConsequence - Adds transcript-specific consequence predictions to a VCF file (similar to Ensembl VEP).
• VcfAnnotateFromBed - Annotates the INFO column of a VCF with data from a BED file.
• VcfAnnotateFromBigWig - Annotates the INFO column of a VCF with data from a BED file.
• VcfAnnotateFromVcf - Annotates a VCF file with data from one or more source VCF files.
• VcfAnnotateHexplorer - Annotates a VCF with Hexplorer and HBond scores.
• VcfAnnotateMaxEntScan - Annotates a VCF file with MaxEntScan scores.
• VcfBreakMulti - Breaks multi-allelic variants into several lines, making sure that allele-specific INFO/SAMPLE fields are still valid.
• VcfCalculatePRS - Calculates the Polgenic Risk Score(s) for a sample.
• VcfCheck - Checks a VCF file for errors.
• VcfExtractSamples - Extract one or several samples from a VCF file.
• VcfFilter - Filters a VCF based on the given criteria.
• VcfLeftNormalize - Normalizes all variants and shifts indels to the left in a VCF file.
• VcfMerge - Merges several VCF files into one VCF.
• VcfSort - Sorts variant lists according to chromosomal position.
• VcfSplit - Splits a VCF into several chunks.
• VcfStreamSort - Sorts entries of a VCF file according to genomic position using a stream.
• VcfSubstract - Substracts the variants in a VCF from a second VCF.
• VcfToBed - Converts a VCF file to a BED file.
• VcfToBedpe - Converts a VCF file containing structural variants to BEDPE format.
• VcfToTsv - Converts a VCF file to a tab-separated text file.

BEDPE tools (structural variants)

• BedpeAnnotateFromBed - Annotates a BEDPE file with information from a BED file.
• BedpeFilter - Filters a BEDPE file by region.
• BedpeGeneAnnotation - Annotates a BEDPE file with gene information from the NGSD (needs NGSD).
• BedpeSort - Sort a BEDPE file according to chromosomal position.
• BedpeToBed - Converts a BEDPE file into BED file.
• SvFilterAnnotations - Filter a structural variant list in BEDPE format based on variant annotations.

Gene handling tools

• GenePrioritization: Performs gene prioritization based on list of known disease genes and a PPI graph (see also GraphStringDb).
• GraphStringDb: Creates simple representation of String-DB interaction graph.
• GenesToApproved - Replaces gene symbols by approved symbols using the HGNC database (needs NGSD).
• GenesToBed - Converts a text file with gene names to a BED file (needs NGSD).
• GenesToTranscripts - Converts a text file with gene names to transcript names (needs NGSD).
• NGSDExportGenes - Lists genes from NGSD (needs NGSD).
• TranscriptsToBed - Converts a text file with transcript names to a BED file (needs NGSD).

Phenotype handling tools

• PhenotypesToGenes - Converts a phenotype list to a list of matching genes (needs NGSD).
• PhenotypeSubtree - Returns all sub-phenotype of a given phenotype (needs NGSD).

Misc tools

• PERsim - Paired-end read simulator for Illumina reads.
• FastaInfo - Basic info on a FASTA file.
• HgvsToVcf - Transforms a TSV file with transcript ID and HGVS.c change into a VCF file (needs NGSD).

ChangeLog

Changes in release 2024_06:

• new tools: NGSDExportIgvGeneTrack
• BamFilter: added parameter for maximum insert size
• NGSDAddVariantsGermline: now imports REs as well
• NGSDExportSamples: new paramters -only_with_small_variants and -add_lab_columns.
• SampleGender: new parameter -include_single_end_reads for long-read data.
• SampleSimilarity: new parameter -include_single_end_reads for long-read data.
• SampleSimilarity: new parameter -roi_hg38_wes_wgs to make WES, WGS and lrGS results more comparable.
• UpdHunter: new parameter -out_informative to write out a IGV track with informative variants.
• VcfCalculatePRS: new parameter -min_depth and support for variants that are to be imputed independent of the sample genotype.
• NGSD:
  • added tables for somatic SVs: somatic_somatic_sv_callset, somatic_sv_deletion, somatic_sv_duplication, somatic_sv_insertion, somatic_sv_inversion, somatic_sv_translocation, somatic_report_configuration_sv
  • added tables for repeat expansions: repeat_expansion, repeat_expansion_genotype, re_callset, report_configuration_re
  • processed_sample table: added boolean scheduled_for_resequencing to flag samples for resequencing to increase depth/coverage

For older changes see releases.