slow5_pod5_converter is a conversion tool for converting (POD5->SLOW5).
Converting a pod5 file to a slow5 file.
Clone via ssh:
git clone --recurse-submodules [email protected]:Sophia-bhs/slow5_pod5_converter.git
Clone via https:
git clone --recurse-submodules https://github.com/Sophia-bhs/slow5_pod5_converter.git
Compilation and Usage
cd slow5_pod5_converter
make clean
make p2s
./p2s path/to/input.pod5 path/to/output.blow5
Please note: The team at Oxford nanopore Technology are often updating their pod5-format module through new releases, and since we include their libraries within our module, it is important that we stay up to date with their changes. See there releases here.
How to update a pod5-format to the latest release
- create a directory in your local environment to hold the new pod5-format release
- download and unzip the new release from the link above
- replace pod5-format files/directories present in our repo with new release versions
The Pod5 file format, developed by Oxford Nanopore Technology, and Slow5 file format, developed by the team at Garvan Institute of Medical Research, both have their benefits, however slow5 format prevails in it's memory efficiency, scalability and it's variety of extensions. This project aims to establish a format conversion tool which will allows users to convert their pod5 files to slow5 and reap the technical benefits. The primary languages used to build this project are C and C++ which ensures a reliable, safe and, principally, a fast conversion.
For more on the Pod5 and Slow5 formats visit SPECIFICATION.md
See DESIGN.md for details on the structure of the project
Convert single pod5 file with 10 reads using slow5-pod5-converter.
> mkdir test/mySlow5
> ./p2s test/examplefile.pod5 test/mySlow5/output.blow5
slow5tools is a toolkit, developed by the team at Garvan, used to visualise and manipulate slow5 files.
Install slow5tools
Follow instructions on setup/install here: https://github.com/hasindu2008/slow5tools Garvan's most recent release of slow5tools is slow5tools-v0.5.0.
> cd slow5tools-v0.5.0
> ./slow5tools view ../slow5_pod5_converter/test/mySlow5/output.blow5 | grep -v ^@ | head -n 10 | cut -f1-7,9-16
#slow5_version 0.2.0
#num_read_groups 1
#char* uint32_t double double double double uint64_t char* double int32_t uint8_t uint64_t
#read_id read_group digitisation offset range sampling_rate len_raw_signal channel_number median_before read_number start_mux start_time
0000173c-bf67-44e7-9a9c-1ad0bc728e74 0 8192 21 1437.697632 4000 123627 109 183.107742 1093 4 4534321
002fde30-9e23-4125-9eae-d112c18a81a7 0 8192 4 1437.697632 4000 37440 463 174.630371 75 2 122095
006d1319-2877-4b34-85df-34de7250a47b 0 8192 6 1437.697632 4000 337876 489 193.573578 1053 4 4347870
00728efb-2120-4224-87d8-580fbb0bd4b2 0 8192 2 1437.697632 4000 161547 147 194.65097 657 2 7231572
007cc97e-6de2-4ff6-a0fd-1c1eca816425 0 8192 23 1437.697632 4000 505057 126 198.097534 1625 2 7820030
008468c3-e477-46c4-a6e2-7d021a4ebf0b 0 8192 4 1437.697632 4000 206976 2 219.046417 411 2 2510647