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/.

Hifiasm-0.15.4 (r343)

1. Integrate the option '--l-msjoin' to detect misjoined unitigs before Hi-C phasing.
2. Further reduce hamming error rate for Hi-C phased assembly.

Hifiasm-0.15.3 (r339)

1. Reduce the hamming error/switch error rate of samples with low heterozygosity rate for both Hi-C phased assemblies and trio-based assemblies.

Hifiasm-0.15.2 (r334)

1. Improved the ability to generate better chromosome-level phased assemblies with Hi-C.

Hifiasm-0.15.1 (r328)

1. Fixed minor bugs for perturbation of Hi-C partition.
2. Fixed bugs for bubble popping when handling complex bubbles, especially for polyploidy samples.
3. In Hi-C phasing module, incorporated the option '--n-weight', which might be more important than '--n-perturb' and '--f-perturb'.
4. Note: the bin files for Hi-C alignment of previous versions cannot be reused.