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ＶｏｌｔＭＲ is pure java NGS (DNA/RNA) mapping and realignment soft that run on Hadoop 2.0 The accuracy is comparable to BWA-MEM and novoalgin with speed faster than those aligner. Using 100 core, VoltMR finish typical exome sample (10GB),mapping, sort, mark duplicate, local realignment in 30 minitue. It use about 10GB to 15GB RAM for each hadoop mapper and reducer.
Currently, VoltMR take fastq as a input and output bam/ADAM format.
For DNA mapping, GATK compatible realignment/recalbration followed after mapping.
For RNA mapping, splice aware algorithm is implemented. Volt is open source, released as "LGPLv3"
Features
- DNA mapping with Realignment/recalibration
- Splice Aware RNA mapping
- BAM/Hadoop-BAM/ADAM output
- DbSNP and ALT region aware reference construction
- Mapping for Virus Integration
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