Hifiasm-0.19.4-r575

Since Hifiasm-0.19.3 (r572):

1. Fixed the bug that haplotype-resolved assemblies may miss a few Mbs regions.

Hifiasm-0.19.3-r572

Since Hifiasm-0.19.1 (r559):

1. Avoided potiential chromosome-level misassemblies for the UL-integration assembly.
2. The assembly graph of polyploidy samples could keep more information.

Hifiasm-0.19.1-r559

Since Hifiasm-0.19.0 (r554):

1. Incorporated two options path-max and path-min for the UL+HiFi assembly. For these two options, higher number may make the assembly cleaner, but may lead to more misassemblies.
2. Removed unnecessary outputs.
3. Please note that to make full use of current release, the second round of UL bin files before hifiasm-0.19.0 (r554) should be reproduced. Given the bin files of HG00544 as an example, all bin files except HG00544.ec.bin, HG00544.ovlp.reverse.bin, HG00544.ovlp.source.bin , and HG00544.ul.ovlp.bin should be deleted.

Hifiasm-0.19.0-r554

Since Hifiasm-0.18.9 (r527):

1. Improved quality for the UL+HiFi assembly with better resoluton of hard-to-assembled regions.

Hifiasm-0.18.9-r527

Since Hifiasm-0.18.8 (r525):

1. Small bug fixed for the ultra-long read alignment.

Hifiasm-0.18.8-r525

Since Hifiasm-0.18.7 (r513):

1. Hifiasm has a more accurate alignment procedure for ultra-long nanopore reads, so that the related bin files cannot be reused. To get the best result with existing bin files produced by previous releases, it would be better to delete the bin files of the ultra-long alignment (*re*bin), and rerun the current release.
2. Updated slightly better Hi-C phasing procedure.

Hifiasm-0.18.7-r513

Since Hifiasm-0.18.5 (r499):

1. Fixed the bug when doing the base-level alignment for homology detection (#394).
2. Printing the clear assembly graph in trio-binning mode for visualization (*p_utg.gfa).
3. The UL+HiC mode will produce silightly different results. The HiC phased assemblies should have better hamming error rates and less false duplications in most cases.

Known issue:

1. Bioconda version of hifiasm is several times slower than the manually built version from the source code (#392). Waiting for the updates from bioconda.

Hifiasm-0.18.5-r499

Since Hifiasm-0.18.4 (r496) beta:

1. Fixed bugs for the haplotype-resolved assembly, which might fragment the assembly. This issue is more serious for the UL-integration assembly. The current release could produce haplotype-resolved assemblies with less number of contigs, higher N50/AuN, and fewer false duplications.
2. Fixed the bug that there are minor differences between assemblies running from scratch and rerunning from the bin files.

Hifiasm-0.18.4-r496 beta

Since Hifiasm-0.18.4 (r496) beta:

1. Fixed bugs for the UL-integration assembly (#367 (comment)).
2. Improved the phasing results for the Hi-C+UL+HiFi assembly.
3. Integrated new option --s-base to enable homology detection in base-level. This might be helpful in improving the Hi-C phasing results for the samples with very high heterozygosity or centromeres.
4. The UL alignment step is 30% faster and the assembly quality of the UL-integration assembly could be improved. The bin files could not be reused.
5. Reconstructed more telomeres.

Hifiasm-0.18.2-r467 beta

Since Hifiasm-0.18.1 (r467) beta:

1. Fixed bugs for the UL-integration assembly that may lead to unbalanced two haplotypes, especially for the Hi-C phased assemblies and the dual assemblies.
2. Fixed bugs for the UL-integration assembly that may output incorrect rd:i in the gfa files.
3. Improve the phasing results for the Hi-C+UL+HiFi assembly.
4. The bin files of Hifiasm-0.18.1 (r466) 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.