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CHANGELOG.md

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Changelog

Unreleased

Changed

  • Fixed the compatibility with TensorFlow 2.2 for the signal scaler model.

[0.5] - 2019-10-18

Added

  • Added a 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 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 are 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 a higher robustness to irregular signals.

[0.4.1] - 2019-02-27

This release fixes the binary packages lacking the essential resource files.

[0.4] - 2019-02-13

Added

  • Poreplex now support multi-read FAST5 files as inputs.
  • FAST5 files which had base-called with the ONT guppy can be used as inputs.

Changed

  • 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.

[0.3.1] - 2018-10-09

This minor release fixes an ABI compatibility issues in the binary packages.

[0.3] - 2018-10-09

Added

  • 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)

Changed

  • 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.