Convolutional coding and basecaller-decoder integration for nanopore sequencing based DNA storage - data
This repository contains data for the experiments corresponding to https://github.com/shubhamchandak94/nanopore_dna_storage/. Some of the files used in the analysis are not available here, but can be generated using the data available here and the scripts available at https://github.com/shubhamchandak94/nanopore_dna_storage/.
Note that the data here is in compressed format and in some cases, hosted outside GitHub. The instructions for downloading/decompressing the data are available in the respective directories.
Directory description:
decoded_lists
: contains the output of the convolutional code decoder for each experiment. These decoded lists are used by the RS outer code decoder to recover the encoded file.encoded_file
: contains the files that were encoded as part of the experiments.fast5_pass
: contains the original raw signal data in the fast5 format.fastq
: contains the basecalled reads.oligo_files
: contains the files containing the oligos that were sent for synthesis (one file for each experiment and a merged file). Also contains the input to the convolutional code encoder, which is helpful for error analysis.raw_data
: contains raw signal data split by experiment, which is used to run the convolutional code decoder.stats
: contains some statistics of the basecalled reads including error rates and read length distribution.