slow5curl

Commands and Options

COMMANDS

• get:
  Retrieve records for specified read IDs from a remote BLOW5 file URL.

• head:
  Print header information from a remote BLOW5 file URL.

• reads:
  Print list of all read IDs from a remote BLOW5 file URL.

get

Retrieve records for specified read IDs from a remote BLOW5 file URL.

slow5curl get [OPTIONS] https://url/to/file1.blow5 readid1 readid2 ....
slow5curl get [OPTIONS] https://url/to/file1.blow5 --list readids.txt

• --to format_type:
  Specifies the format of output files. format_type can be slow5 for SLOW5 ASCII or blow5 for SLOW5 binary (BLOW5) [default value: blow5].
• -o FILE, --output FILE:
  Outputs data to FILE [default value: stdout]. This can auto detect the output format from the file extension.
• -c, --compress compression_type:
  Specifies the compression method used for BLOW5 output. compression_type can be none for uncompressed binary; zlib for zlib-based (also known as gzip or DEFLATE) compression; or zstd for Z-standard-based compression [default value: zlib]. This option is only valid for BLOW5. zstd will only function if slow5curl has been built with zstd support which is turned off by default.
• -s, --sig-compress compression_type:
  Specifies the raw signal compression method used for BLOW5 output. compression_type can be none for uncompressed raw signal or svb-zd to compress the raw signal using StreamVByte zig-zag delta [default value: svb-zd]. Note that record compression (-c option above) is still applied on top of the compressed signal. Signal compression with svb-zd and record compression with zstd is similar to ONT’s vbz. zstd+svb-zd offers slightly smaller file size and slightly better performance compared to the default zlib+svb-zd, however, will be less portable.
• -t, --threads INT:
  Number of threads (connections) [default value: 128]. As these threads are for network access, the number of threads can be much larger than the number of CPU threads available on the system. The max number of threads will typically depend on the request limit of the server. For example, we may go up to 512 threads, but if the server only allows 128 requests at a time per client, we will be limited by the latter.
• -K, --batchsize:
  The batch size. This is the number of records on the memory at once [default value: 4096]. An increased batch size improves multi-threaded performance at the cost of higher RAM.
• -l, --list FILE:
  List of read ids provided as a single-column text file with one read id per line.
• -r, --retry INT:
  Number of times to retry a fetch before aborting the program [default value: 1]. These are a rare occurance and thus should be kept a low number. If a fetch fails twice in a row it is likely that something has gone wrong with the connection/server, or the client is being denied further access to the remote BLOW5.
• -w, --wait INT:
  Number of seconds to wait before retrying a fetch [default value: 1].
• --skip:
  Warn and continue if a read_id was not found
• --index FILE:
  URL to a custom slow5 index. Useful if your index file is located somewhere other than https://url/file.blow5.idx when your input file is https://url/file.blow5. This can also be a path to an index that is residing locally on your disk. Useful if you want to repeatedly query the same BLOW5 file and want to avoid repeated index downloads.
• --cache FILE:
  Save the downloaded index to the specified file path. This can be referenced later using –index option to avoid downloading the same index file.
• -h, --help:
  Prints the help menu.

head

Print header information from a remote BLOW5 file URL.

slow5curl head https://url/to/file1.blow5

reads

Print the list of read IDs from a remote BLOW5 file URL.

slow5curl reads https://url/to/file1.blow5

• --cache FILE:
  Save the downloaded index to the specified path. This can be referenced later to avoid downloading the same index file.

GLOBAL OPTIONS

• -V, --version:
  Print the slow5curl version number.
• -v INT, --verbose INT:
  Set the verbosity level (0-6) [default value: 4]. 0-off, 1-errors, 2-warnings, 3-information, 4-verbose, 5-debug, 6-trace.
• -h, --help:
  Prints the help menu.
• --cite:
  Prints the citation information.

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