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- cutadapt software: cutadapt.readthedocs.io
- bowtie software: bowtie-bio.sourceforge.net
- samtools software: samtools.sourceforge.net
- Biopython: biopython.org
- Davies2016
Davies J.O. et al., "Multiplexed analysis of chromosome conformation at vastly improved sensitivity" Nature Methods 13 (2016)
- Hughes2014
Hughes J.R. et al., "Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment" Nature Genetics 46 (2014)
- Langmead2009
Langmead B. at al., "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome" Genome Biology 10 (2009)
- Li2009
Li H. et al., "The Sequence Alignment/Map format and SAMtools" Bioinformatics 25 (2009)
- Martin2011
Martin M. "Cutadapt removes adapter sequences from high-throughput sequencing reads" EMBnet.journal 17 (2011)
- capC-MAP
Brackley C.A. et al., "capC-MAP : Analysis software for Capture-C data" (2018)