distmap

distmap performs distributed short-read mapping of next-generation sequencing data (e.g., Illumina HiSeq) to enable scalable alignment for downstream genomic analyses.

Key Features:

• Modular and Scalable Workflow: Implements a modular system that distributes computational tasks across multiple nodes in a Hadoop cluster for scalable processing of large datasets.
• Support for Multiple Mapping Tools: Integrates nine different short-read mapping tools to provide algorithmic flexibility for diverse data characteristics.
• Cross-Platform Compatibility: Runs on Unix-based operating systems commonly used in bioinformatics computing environments.
• Input and Output Formats: Accepts input reads in FASTQ format and outputs alignments in SAM/BAM formats for downstream analysis.
• Read Types Supported: Processes both paired-end and single-end sequencing reads.

Scientific Applications:

• Genome Assembly: Provides scalable alignment of short reads to support genome assembly workflows.
• Variant Calling: Generates mapped reads in SAM/BAM formats suitable for variant detection and genotyping pipelines.
• Transcriptome Analysis: Enables alignment of RNA-seq short reads for transcriptome profiling and expression analysis.
• Metagenomic Studies: Supports large-scale short-read mapping for taxonomic and functional analysis in metagenomics.

Methodology:

Operates within the Hadoop distributed computing framework to parallelize mapping tasks across a cluster and integrates nine short-read mapping tools for alignment.