Poreplex 0.5

Added

• Added support for basecalls from the Guppy's flip-flop model.
• --fast5 now writes multi-read FAST5 files by default. --symlink-fast5 is removed as symbolic links are not compatible with multi-read FAST5s.
• Barcode accuracy is calibrated and reported for every read in barcode_score within sequencing_summary.txt in the phred-scale.
• For the dashboard view, the first part delimited by '|' of identifier in the minimap2 index is used for display or mapping to transcript names.
• Poreplex now stops processing when it seems that the whole bunch of FAST5 files is not basecalled. (It stops on the 1000th non-basecalled read while no read had been processed correctly.)

Changed

• The barcode demultiplexer is updated to provide calibrated accuracy predictions and higher robustness to irregular signals.

Poreplex 0.4.1

This minor update fixes a problem in the binary packages.

(from 0.4)

• Poreplex now supports multi-read FAST5 files as inputs.
• FAST5 files which had base-called with the ONT guppy can be used as inputs.
• Fixed filename in sequencing_summary.txt points to wrong locations of
  FAST5 files when both FAST5 output and barcoding are turned on.
• Poly(A) dwell time measurement is now more robust to pepper and salt
  noises.
• Fixed BAM alignment writers which had generated broken files in
  multi-threaded processing.

Poreplex 0.4

• Poreplex now supports multi-read FAST5 files as inputs.
• FAST5 files which had base-called with the ONT guppy can be used as inputs.
• Fixed filename in sequencing_summary.txt points to wrong locations of
  FAST5 files when both FAST5 output and barcoding are turned on.
• Poly(A) dwell time measurement is now more robust to pepper and salt
  noises.
• Fixed BAM alignment writers which had generated broken files in
  multi-threaded processing.

Poreplex 0.3.1

Changes in 0.3.1

• Fixes an ABI compatibility issue in the binary packages

New features in 0.3

• Reads now can be demultiplexed without basecalling.
• With --polya turned on, poly(A) tail dwell time is written to sequencing_summary.txt. More detailed information is written to the dumped events by the --dump-basecalled-events switch.
• Shows detailed error messages in poreplex.log.
• The files generated by --dump-basecalled-events now includes the attributes for signal scaling parameters and the last position that DNA adapter ends within the signal.
• Extremely short sequences are now sorted into failed reads. The minimum required length can be changed with the --minimum-length switch. (Suggested by Nathan Roach)

Changes in 0.3

• Fixed a segmentation fault when using albacore 2.3.3.
• Fixed an error that stops overall process by an invalid FAST5 file.
• filename in sequencing_summary.txt is now shown as a relative path from the output directory, not from the subdirectory for a read group.
• Fixed a problem that separate lines of FASTA, FASTQ or sequencing-summary.txt are mixed up in the output file sometimes.
• Turned off the chimeric read filter by default. Now the --filter-chimera option turns it back on.
• Updated the neural network model for barcode demultiplexing for even less false positives using randomly stitched signal fragments as a background.

Poreplex 0.3

New features in 0.3

• Reads now can be demultiplexed without basecalling.
• With --polya turned on, poly(A) tail dwell time is written to sequencing_summary.txt. More detailed information is written to the dumped events by the --dump-basecalled-events switch.
• Shows detailed error messages in poreplex.log.
• The files generated by --dump-basecalled-events now includes the attributes for signal scaling parameters and the last position that DNA adapter ends within the signal.
• Extremely short sequences are now sorted into failed reads. The minimum required length can be changed with the --minimum-length switch. (Suggested by Nathan Roach)

Changes in 0.3

• Fixed a segmentation fault when using albacore 2.3.3.
• Fixed an error that stops overall process by an invalid FAST5 file.
• filename in sequencing_summary.txt is now shown as a relative path from the output directory, not from the subdirectory for a read group.
• Fixed a problem that separate lines of FASTA, FASTQ or sequencing-summary.txt are mixed up in the output file sometimes.
• Turned off the chimeric read filter by default. Now the --filter-chimera option turns it back on.
• Updated the neural network model for barcode demultiplexing for even less false positives using randomly stitched signal fragments as a background.

Poreplex version 0.2

Changes in this version:

• Added LICENSE.txt to the source distribution.
• Added a long description for the PyPI project entry.

The first release (version 0.1)

This is the first alpha release of poreplex.