NGSUtils
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Application data |
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| Created by | Breese MR, Liu Y |
|---|---|
| Biological application domain(s) | Genomics, Transcriptomics |
| Principal bioinformatics method(s) | Sequence contamination filtering, Sequencing quality control, Read pre-processing, Variant calling, Formatting |
| Technology | Illumina, ABI SOLiD |
| Created at | Indiana University |
| Maintained? | Yes |
| Input format(s) | BAM, (Compressed) FASTQ, GTF, BED |
| Programming language(s) | Python |
| Licence | GPL |
| Operating system(s) | Linux, Mac OS X |
Summary: NGSUtils is a suite of software tools for working with next-generation sequencing datasets
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Description
NGSUtils is a suite of software tools for working with next-generation sequencing datasets. Staring in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working with next-generation sequencing data. We initially started doing custom coding for each project in a one-off manner. It quickly became apparent that this was an inefficient manner to work, so we started assembling smaller utilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia, SOLiD and 454 sequencing data. We have used them for DNA and RNA resequcing, ChIP-seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting). These tools are also used heavily in our in-house DNA and RNA mapping pipelines.
These tools have of great use within our lab group, and so we are happy to make them available to the greater community.
NGSUtils is made up of 50+ programs, mainly written in Python. These are separated into modules based on the type of file that is to be analyzed. There are four modules:
bamutils (BAM/SAM files) bedutils (BED files) fastqutils (FASTQ files, base- and color-space) gtfutils (GTF gene models)
Links
References
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