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ngs-bits - Short-read sequencing tools

Linux build status MacOS build status Windows build status
install with bioconda

Obtaining ngs-bits

Binaries of ngs-bits are available via Bioconda:

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 2022_07
> 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

ChangeLog

Changes in release 2022_07:

  • VcfAnnotateFromVcf: refactoring of command line parameters and updated documentation.
  • SampleSimilarity: changed number of SNPs for BAM mode, MODIFIER impact variants are now ignored in GSvar mode to make scores more similar between exomes and genomes, updated documentation.
  • MappingQC: added metrics for uniformity of coverage in WGS mode.
  • HgvsToVcf: Added handling of unnecessary sequences in 'delins', added support for dup/del with trailing sequence.
  • VcfSort: files without FORMAT/SAMPLE columns are can now be processed without adding the column.
  • VcfLeftNormalize: improved runtime when 'stream' parameter is not used.
  • added tools: VcfAnnotateHexplorer, HgvsToVcf, VcfAnnotateConsequence
  • NGSD:
    • transcript: added biotype, MANE Select flag, MANE Plus Clinical flag, Ensembl canonical flag.
    • variant: removed 1000g AF.
    • sample: added patient identifer, added tissue enum.

For older releases see the releases page.

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:

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.

BAM tools

  • BamClipOverlap - (Soft-)Clips paired-end reads that overlap.
  • BamDownsample - Downsamples a BAM file to the given percentage of reads.
  • BamFilter - Filters a BAM file by multiple criteria.
  • BamHighCoverage - Determines high-coverage regions in a BAM file.
  • BamToFastq - Converts a BAM file to FASTQ files (paired-end only).

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)

  • 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.
  • 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.
  • VcfSort - Sorts variant lists according to chromosomal position.
  • VcfStreamSort - Sorts entries of a VCF file according to genomic position using a stream.
  • 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)

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).
  • NGSDExportGenes - Lists genes from NGSD (needs NGSD).

Phenotype handling tools

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).

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