NGSmethPipe
NGSmethPipe is a program for the generation of single base-pair-resolution methylation maps from bisulfite conversion high throughput sequencing experiments. The program has 4 steps: i. indexing (sequence conversion into 3 letter alphabet building the Bowtie index), ii. preprocessing of the reads (adapter removal, quality trimming), iii. Bowtie alignment (single-end or pair-end reads) and vi. post-processing including SNV and bisulfite failure detection, sequence error handling and extraction of methylation data for different sequence contexts.
Main features of NGSmethPipe
1. The program implements three quality filters: i. putative bisulfite failures can be detected, ii. the false positive rate can be controlled by means of the Phred Scores, iii. SNV (single nucleotide variants) can be detected and removed.
2. Usage of a “seed extension” method applied to the Bowtie alignments allowing to map a higher number of reads without compromising the mapping quality.
3. Extensive output options including all possible cytosine sequence contexts ( CG, CHG and CHH; where H is A, T or C) and the possibility to join the information from both strands (useful for the detection of hemi-methylation).
4. Complete statistics of the whole process, including aligned reads, discarded reads, discarded positions, chromosome data coverage, etc.
5. The memory and CPU needs can be adapted to the user’s computer resources.
6. Fastq input files are accepted in zip, gzip, bzip2 or uncompressed.
[1] Michael Hackenberg, Guillermo Barturen and José L. Oliver. 2012. DNA Methylation Profiling from High-Throughput Sequencing Data In: DNA Methylation – From Genomics to Technology Dr. Tatiana Tatarinova (Ed.), ISBN: 978-953-51-0320-2, InTech [PDF]