Hifiasm-0.18.1-r466 beta

Since Hifiasm-0.18.0 (r461) beta:

1. Fixed bugs for the UL-integration assembly that may lead to assertion failure.
2. Could produce the cleaner assembly graph with UL reads.
3. Improve the phasing results for the Hi-C+UL+HiFi assembly.
4. Slightly improve the assembly quality for the homozygous sample.
5. The bin files of Hifiasm-0.18.0 (r461) could be reused.

Please note that this mode is not stable. There are several known issues to be fixed:

1. The UL + HiC + HiFi might introduce higher numbers of hamming errors.
2. Only well-tested with >=100kb UL reads.
3. The QV could be further improved.

Hifiasm-0.18.0-r465 beta

Since Hifiasm-0.17.7 (r461) beta:

1. Fixed bugs for the UL-integration assembly when the coverage of UL is relatively low. Could reuse the bin files of Hifiasm-0.17.7 (r461).
2. Improve the phasing results for the Hi-C+UL+HiFi or Hi-C+HiFi. Could reuse the bin files of Hifiasm-0.17.7 (r461).

Please note that this mode is not stable. There are several known issues to be fixed:

1. The UL + HiC + HiFi might introduce higher numbers of hamming errors.
2. Only well-tested with >=100kb UL reads.
3. The QV could be further improved.

Hifiasm-0.17.7 (r461) beta

Since Hifiasm-0.17.7 (r461) beta:

1. Slightly improved the assembly graph and the final contigs.

Please note that this mode is not stable. There are several known issues to be fixed:

1. The UL + HiC + HiFi might introduce higher numbers of hamming errors.
2. Only tested with >=100kb UL reads.
3. The QV could be further improved.

Hifiasm-0.17.6 (r460) beta

Issue fixed since Hifiasm-0.17.5 (r458) beta:

1. Fixed the bug when aligning UL reads, which affects all procedures of the UL-integration assembly. It would be better to rerun the UL assembly from the scratch (delete all bin files except ec.bin, ovlp.reverse.bin, and ovlp.source.bin).

Please note that this mode is not stable. There are several known issues to be fixed:

1. The UL + HiC + HiFi might introduce higher numbers of hamming errors.
2. Only tested with >=100kb UL reads.
3. The QV could be further improved.

Hifiasm-0.17.5 (r458) beta

Issues fixed since Hifiasm-0.17.4 (r455) beta:

1. The gap-filling procedure with UL reads is more accurate.
2. Fixed memory leaks.

Please note that this mode is not stable. There are several known issues to be fixed:

1. The UL + HiC + HiFi might introduce higher numbers of hamming errors.
2. Only tested with >=100kb UL reads.
3. The QV could be further improved.

Hifiasm-0.17.3 (r452) beta

Integrated the new ultra-long ONT integration mode with the option --ul. Please note that this mode is not stable right now. There are several known issues to be fixed:

1. The UL + HiC + trio might introduce higher numbers of hamming errors.
2. The gap-filling procedure with UL reads might be not accurate.
3. Haven't tested with the haploid genome (will update soon).
4. The QV could be further improved.

Hifiasm-0.17.4 (r455) beta

Integrated the new ultra-long ONT integration mode with the option --ul. Please note that this mode is not stable right now. There are several known issues to be fixed:

1. The UL + HiC + trio might introduce higher numbers of hamming errors.
2. The gap-filling procedure with UL reads might not be accurate.
3. Only tested with >=100kb UL reads.
4. The QV could be further improved.

Issues fixed since Hifiasm-0.17.3 (r452) beta:

1. Bugs for the bubble chain renewal.
2. Adjusted parameters for the haploid genome.

Hifiasm-0.16.1 (r375)

1. Improved Hi-C phasing around centromeres.
2. Fixed bugs for missing unitigs during Hi-C phasing assembly or trio-binning assembly (#159).

Hifiasm-0.16.0 (r369)

1. Improved the error correction part by better seeding. This release may improve the contig N50 and the resolution of repetitive regions. Please note that this release is not compatible with the bin files produced by old versions.
2. Integrated the option --hg-size. It is used to infer read coverage accurately.
3. Integrated the option --max-kocc.

Hifiasm-0.15.5 (r350)

1. Fixed bugs for too small dataset (#152) and too large dataset (#136).
2. Removed the option --purge-cov. It was replaced by two new options --hom-cov and --purge-max.
3. Hifiasm can automatically update bin files for Hi-C phasing if the unitig graph is updated. Users must manually delete bin files using previous versions, which is confusing.
4. Added a complete documentation at https://hifiasm.readthedocs.io/en/latest/.