NGseqBasic - a single-command UNIX tool for ATAC-seq, DNaseI-seq, Cut-and-Run, and ChIP-seq data mapping, high-resolution visualisation, and quality control

• DOI: 10.1101/393413
• Publication Date: 2018-08-16T14:55:10Z
• Authors: Jelena Telenius; ; Jim R. Hughes
• Keywords: Disk formatting

ABSTRACT With decreasing cost of next-generation sequencing (NGS), we are observing a rapid rise in the volume ‘big data’ academic research, healthcare and drug discovery sectors. The present bottleneck for extracting value from these sets is data processing analysis. Considering this, there still lack reliable, automated easy to use tools that will allow experimentalists assess quality sequenced libraries explore first hand, without need investing lot time computational core analysts early stages NGseqBasic an easy-to-use single-command analysis tool chromatin accessibility (ATAC, DNaseI) ChIP data, providing support also new techniques such as low cell number Cut-and-Run. It takes fastq, fastq.gz or bam files, conducts all control, trimming mapping steps, along with control statistics, combines this single-click loadable UCSC hub, integral statistics html page detailed reports metrics. set up, no installation needed. A wide variety parameters provided fine-tune analysis, optional setting generate DNase footprint high resolution ChIP-seq tracks. tester script help setup, test downloadable example user cases. has been used routine next generation (NGS) high-impact publications 1,2 . code actively developed, accompanied Git version Github repository. Here demonstrate features using DNaseI-seq GSM689849, CTCF-ChIP-seq GSM2579421, well Cut-and-Run CTCF GSM2433142, provide one-click hubs generated by tool, allowing ready exploration run results files tool. Availability Download, setup instructions available on web site http://userweb.molbiol.ox.ac.uk/public/telenius/NGseqBasicManual/external/ Bioconda users can load library “ngseqbasic”. source https://github.com/Hughes-Genome-Group/NGseqBasic/releases Contact [e-mail]