fast5tools 0.4

Tools for working with fast5 files (Oxford Nanopore DNA/RNA sequencing data).

Add the fast5tools dir to your PYTHONPATH. Add fast5tools/bin to your PATH

Try:

$ git clone https://github.com/JohnUrban/fast5tools.git

$ cd fast5tools

$ FAST5TOOLS=${PWD}

$ FAST5TOOLSPATHS=${FAST5TOOLS}:${FAST5TOOLS}/bin:${FAST5TOOLS}/fast5tools

$ export PATH=${FAST5TOOLSPATHS}:$PATH

$ export PYTHONPATH=${FAST5TOOLSPATHS}:$PYTHONPATH

$ python setup.py test

This will test various fast5 files in rundata/ that span from the beginning of MAP to recently. It is actually running tests/testf5_class.py on them.

Scripts are available in the bin directory and may be run as command line programs once fast5tools is installed.

All scripts can read:

• a single fast5
• many fast5s listed in a row
• a file-of-file-names (with .fofn extension) of fast5s
• a tarchive with fast5s in dirs and subdirs
• acombination of those

Fast5 information:

• fast5attributes.py

Fast5 stats:

• fast5stats.py - generate a table with any fast5 info you want.
• fast5TableSummary.py -- in progress -- The intention was to be able to give summary stats for any table with any fast5 info in any order (so long as you can tell it the order).
• fast5standardSummary.py

Plotting from stats tables:

• fast5plot.py -- in progress.

Plotting (and kmer counting/plotting) from fast5s directly:

• fast5ReadLengthPlots.py
• fast5_qual_histogram.py
• fast5_qual_v_pos_boxplot.py
• fast5plotEvents.py
• fast5plotRaw.py
• kmerCountsFromFastx.py

Extracting Fasta/Fastq:

• fast5Tofastx -- convert to fasta, fastq, quals, integer quals -- or just details about the seqs (similar to fast5stats)
• fast5DerivedFastxMoleculeStats.py

Extracting events, raw data, model information:

• fast5ToEvents.py
• fast5ToModelinfo.py
• fast5toRaw.py

De-barcoding:

• fast5_sw_alignment_viz.py
• fast5_sw_bardecoder.py

Other:

• fast5staypos.py - get position of basecall "stays" in read (e.g. as performed in analyses in biorxiv paper below)
• fast5_regex_parser.py - identify positions of a regex in reads (e.g. as performed in analyses in biorxiv paper below)

Please cite fast5tools as:

Urban JM, Foulk MS, Bliss JE, Coleman CM, Lu N, Mazloom R, Brown SJ, Spradling AC, Gerbi SA. 2020.

Single-molecule sequencing of long DNA molecules allows high contiguity de novo genome assembly for the fungus fly, Sciara coprophila.

bioRxiv 2020.02.24.963009.

https://www.biorxiv.org/content/10.1101/2020.02.24.963009v1

This paper contains the first description of Fast5Tools.

Please cite poreminion as:

Urban, J. M., Bliss, J., Lawrence, C. E. & Gerbi, S. A.

Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION. 2015.

bioRxiv (Cold Spring Harbor Labs Journals, 2015). doi:10.1101/019281

http://biorxiv.org/content/early/2015/05/20/019281

This paper contains the first descriptions and uses of poreminion.