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gene expression, transcription factor, and methylation analysis of next-generation sequencing (ngs) data, including rna-seq and chip-seq

high-throughput sequencing methods generate large amounts of sequence data and require robust computational tools for further analysis. bioinformatics toolbox™ provides algorithms to support common analysis workflows for next-generation sequencing (ngs) data, such as filtering and trimming reads, mapping reads to references, counting the number of reads mapped to genomic features, and performing statistical analyses.

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  • import next-generation sequencing (ngs) data and feature annotations from sam, bam, fasta, fastq, gtf, and gff files

  • manage ngs data with single- and paired-end reads, filter and trim reads, and display quality statistics

  • map reads to reference sequences

  • read summarization and statistical analyses on rna-seq and chip-seq data

  • visualize alignment of reads to reference sequences
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