meRanTK

meRanTK is a versatile high performance toolkit for complete analysis of methylated RNA data.

meRanTK includes the following programs:

• meRanT, a bisulfite aware short read aligner using a set of transcripts as reference (e.g. refSeq)
• meRanG, a bisulfite aware short read aligner using the whole genome as reference
• meRanCall, a methylation caller for precise identification of m⁵Cs from RNA-BSseq or Aza-IP data
• meRanCompare, an experiment comparison tool for identifying significant differentially methylated cytosines from RNA-BSseq or Aza-IP data, supports replcate handling
• meRanAnnotate, an annotation tool for methylated cytosines

The tools can make use of multiprocessing which enables a shorter computing time.

Together they facilitate transcriptome wide identification of methylated cytosines on RNAs a single base pair resolution.
The aligners, meRanT and meRanG, are designed to work with either single- or paired end sequence reads from strand specific RNA-BSseq libraries. Input files may originate from any high throughput sequencing platform that produces standard FASTQ formatted sequence reads (e.g. Illumina, Ion Proton, Ion Torrent). The BAM or SAM output files serve as input files for the meRanCall methylation caller which aims to precisely identify the positions of methylated cytosines from RNA-BSseq or Aza-IP.
Intensive testing demonstrated that meRanTK produces alignmets with high sensitivity and specificitys. Moreover, m⁵C's candidates are statsistically evaluated and so detected with high confidence level resulting in a very low false positive rate. Thus, meRanTK outperforms other BS-RNA tools in terms of specificity and enables researches to obtain more reliable data.

All five programs are written in the Perl programing language and run therefore on a wide variety of computing platforms.