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 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 (NGS'2016 poster).
• ReadQC - Quality control tool for FASTQ files (output is qcML).
• MappingQC - Quality control tool for a BAM file (output is qcML).
• VariantQC - Quality control tool for a VCF file (output is qcML).
• 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.

• BamClipOverlap - Clips paired-end reads that overlap.
• 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.

• 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.
• 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 BED file.
• VcfLeftAlign - Left-aligns indel variants in repeat regions.
• VcfSort - Sorts variant lists according to chromosomal position.