title: MethylCoder: software pipeline for bisulfite-treated sequences.
abstract: BACKGROUND
  MethylCoder is a software program that generates per-base methylation data given a set of bisulfite-treated reads. It provides the option to use either of two existing short-read aligners, each with different strengths. It accounts for soft-masked alignments and overlapping paired-end reads. MethylCoder outputs data in text and binary formats in addition to the final alignment in SAM format, so that common high-throughput sequencing tools can be used on the resulting output. It is more flexible than existing software and competitive in terms of speed and memory use.
  
  
  BACKGROUND
  MethylCoder requires only a python interpreter and a C compiler to run. Extensive documentation and the full source code are available under the MIT license at: https://github.com/brentp/methylcode.
  
  
  BACKGROUND
  bpederse@gmail.com.
authors: Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA. bpederse@gmail.com
authors: Brent
authors: B
authors: Pedersen
authors: Tzung-Fu
authors: TF
authors: Hsieh
authors: Christian
authors: C
authors: Ibarra
authors: Robert L
authors: RL
authors: Fischer
mesh_terms: D003596:Cytosine / Q000378:metabolism; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D019175:DNA Methylation; D023281:Genomics / Q000379:methods; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA; D012984:Software; D013447:Sulfites
chemical_list: D013447:Sulfites; D003596:Cytosine; D004247:DNA; C042345:hydrogen sulfite