Short-read sequencing tools
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README.md

ngs-bits - Short-read sequencing tools

TravisCI status install with bioconda

Obtaining ngs-bits

Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources:

ChangeLog

Changes already implemented in HEAD for next release:

  • Added tools: VcfBreakMulti.

Changes in release 2018_10:

  • Expecting VEP instead of SnpEff annotations in VCFs now (VariantQC, SomaticQC, RohHunter).
  • Added GRCh38 support (MappingQC, SomaticQC, SampleGender, SampleSimilarity).
  • Added tools: SampleAncestry, VcfCheck.

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.

Tools list

ngs-bits contains a lot of tools that are used for NGS-based diagnostics in our institute:

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.
  • 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.
  • BedInfo - Prints summary information about a BED file.
  • BedIntersect - Intersects two BED files.
  • 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.
  • 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

  • VcfAnnotateFromBed - Annotates the INFO column of a VCF with data from a BED file.
  • VcfBreakMulti - Breaks multi-allelic variants into several lines, making sure that allele-specific INFO/SAMPLE fields are still valid.
  • VcfCheck - Checks a VCF file for errors.
  • VcfFilter - Filters a VCF based on the given criteria.
  • VariantFilterRegions - Filter a variant list based on a target region.
  • 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.

NGSD-based tools

Some of the tools need the NGSD, a MySQL database that contains for example gene, transcript and exon data.
Installation instructions for the NGSD can be found here.

Other tools

  • PERsim - Paired-end read simulator for Illumina reads.
  • FastaInfo - Basic info on a FASTA file.