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.

Hifiasm-0.15 (r327)

1. Improved Hi-C phasing module. Incorporated the options '--n-perturb', '--f-perturb' and '--seed' for Hi-C phasing module.
2. Changed the default outputs of hifiasm. Hifiasm outputs a primary assembly and two balanced haplotypes in default. Incorporated the option '--primary' to output primary assembly and alternate assembly.
3. Improved purge_dups module which keeps more hard regions. It applies '-l3' for purge_dups in default.
4. Reduced false duplications in haplotype-resolved assemblies.
5. Note: the bin files for Hi-C alignment of previous versions cannot be reused.
6. Note: please avoid using 0.15 since it is extremely slow when handling complex bubbles.

Hifiasm-0.14.2 (r315)

1. Slightly reduce misassemblies.

Hifiasm-0.14.1 (r314)

This release is mainly used to fix a serious bug.

1. Fixed the serious bug that may duplicate some regions in contigs, especially when doing haplotype-resolved assembly.
2. Incorporated the option '-l3' which is able to purge samples with high heterozygosity rate.
3. Remove the option '--high-het'.

Hifiasm-0.14 (r312)

1. Improved contig N50, and reduced hamming error rate/switch error rate of haplotype-resolved assembly (trio/Hi-C phased).
2. Incorporated the options '--b-cov', '--h-cov' and '--m-rate' to break contigs at potential misassemblies.
3. Incorporated experimental Hi-C phased mode for diploid samples. See the options '--h1' and '--h2'.
4. Incorporated the option '--min-hist-cnt' to ignore noise when analyzing the k-mer spectrum. See 'man ./hifiasm.1'.
5. Fixed bugs for purge_dups and circle length.
6. Make the option '-z' work.

Hifiasm-0.13 (r308)

1. Improved base accuracy (QV) of assembly.
2. Incorporated the option '--lowQ' to print contig regions with low base accuracy and related reads. It might be useful for polishing.
3. Fixed the bug that cannot output circles.

Hifiasm-0.12 (r304)

1. Fixed small bug for primary assembly.