MethylCoder statistics

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MethylCoder specifications


Unique identifier OMICS_00585
Name MethylCoder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output format SAM, tab-delimited text
Operating system Unix/Linux
Programming languages C, Python
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Brent Pedersen <>

Publication for MethylCoder

MethylCoder in pipeline

PMCID: 3983033
PMID: 24721906
DOI: 10.1371/journal.pgen.1004250

[…] features by computing log2(signal/control). for the histone marks, a similar approach was taken, using all available pan-h3 datasets (2 in total)., bisulfite sequencing reads were processed using methylcoder , with “mismatches = 0”, and bowtie to align the reads, with “-m 1 best tryhard -v 2 chunkmbs 1024”. a coverage profile was computed by selecting only methylation context ‘cg’ for cpg […]

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MethylCoder in publications

PMCID: 5747346
PMID: 29333247
DOI: 10.5256/f1000research.14317.r28483

[…] are then counted for all the mapped reads. a number of software tools have been developed for the purposes of read mapping and methylation calling of bs-seq data. popular ones include bismark , methylcoder , brat , bs-seeker and bsmap . most of the software tools rely on existing short read aligners, such as bowtie ., typical downstream dna methylation studies often involve finding […]

PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] bs-seq aligners were also developed to map the bs-seq reads. among these tools, two alternative approaches have been widely used. the three-letter aligners (such as bismark, brat, bs-seeker, and methylcoder) simplify the alignment by converting all cs into ts for the bs-seq reads and both strands of the reference genome (only three alphabets of a, g, and t remaining in the converted […]

PMCID: 4896272
PMID: 26961371
DOI: 10.1186/s12859-016-0910-3

[…] somehow compressed on-the-fly by the caller itself., these problems have been handled by existing tools to various degrees of efficiency. software such as bismark [], brat-bw [], bs-seeker 2 [], and methylcoder [] adopt the approach of converting both genome and reads files to a reduced alphabet, turning all cs into ts (and gs into as while aligning the reversed reads), and calling a standard […]

PMCID: 4425964
PMID: 25921777
DOI: 10.14814/phy2.12358

[…] the library. samples were multiplexed six per lane on a 300 gb flowcell and paired-end sequenced with an illumina hiseq 2000., sequence reads obtained from illumina hiseq 2000 were analyzed by methylcoder (pedersen et al. ) using the genomic short-read-nucleotide alignment program (gsnap) (langmead et al. ; wu and nacu ). bisulfite conversion rates were estimated from the number […]

PMCID: 4009243
PMID: 24839440
DOI: 10.1155/2014/472045

[…] to a reference genome)., many tools have been developed to tackle this computational challenge such as maq [], bismark [], bsmap [], pash [], rmap [], gsnap [], novoalign [], bfast [], brat-bw [], methylcoder [], cokusalignment [], bs-seeker [], bs-seeker2 [], segemehl [], biss [], batmeth [], and the latest one erne-bs5 []. the majority of these bisulfite sequencing mappers first conduct […]

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MethylCoder institution(s)
Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
MethylCoder funding source(s)
National Institute of Health grant R01-GM069415

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