There are no binary releases yet.
Please use git to download the most recent development version:
git clone --recursive https://github.com/imgag/ngs-bits.git
If you are behind a proxy that block the standard git port, you see something like this:
$ git clone --recursive https://github.com/imgag/ngs-bits.git
Cloning into 'ngs-bits'...
fatal: Unable to look up github.com (port 9418) (Name or service not known)
Then you have to adapt your ~/.gitconfig file like that:
[http]
proxy = http://[user]:[password]@[host]:[port]
ngs-bits depends on the following software to be installed
- g++
- qmake (Qt 5.3 or higher, including xmlpatterns and mysql package)
- git (to extract the version hash)
- cmake (to build the bamtools library)
- optional: python and matplotlib (for plot generation in QC tools)
For example, the installation of the dependencies using Ubuntu 14.04/16.04 looks like that:
> sudo apt-get install g++ qt5-default libqt5xmlpatterns5-dev libqt5sql5-mysql git cmake python python-matplotlib
Just execute the following make commands:
make build_3rdparty
make build_tools_release
Now the executables and all required libraries can be found in the bin/ folder!
Note: Instructions how to build ngs-bits unter Windows can be found here.
Please report any issues or questions to the ngs-bits issue tracker.
ngs-bits contains a lot of tools that we use for NGS short-read data analysis in our institute. Not all of these tools are mature enough for public use. Thus, here we will list tools that can be safely used:
- SeqPurge - A highly-sensitive adapter trimmer for paired-end short-read data (paper, poster from ECCB 2016 with more recent benchmarks).
- SampleCorrelation - Calculates the variant overlap and correlation of two VCF/BAM files.
- SampleGender - Determines sample gender based on a BAM file.
- PERsim - Paired-end read simulator for Illumina reads.
- CnvHunter - CNV detection from targeted resequencing data using non-matched control samples.
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. Examplary data for download: tumor-normal.zip.
- BamClipOverlap - (Soft-)Clips paired-end reads that overlap.
- BamDeduplicateByBarcode - Deduplicate a BAM file based on given molecular barcodes.
- BamDownsample - Downsamples a BAM file to the given percentage of reads.
- BamIndex - Creates a BAI index for a BAM file.
- BamLeftAlign - Left-aligns indels in repeat regions.
- BamToFastq - Converts a BAM file to FASTQ files (paired-end only).
- BedAdd - Adds the regions in two BED files.
- 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).
- 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.
- 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.
- 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.