Hifiasm-0.19.9-r616

Since Hifiasm-0.19.8 (r603):

1. Fixed several issues that may lead to segmentation fault.
2. To produce more T2T contigs/scaffolds, there are multiple new options that can keep telomeres at the ends of contigs/scaffolds, including --telo-m, --telo-p, --telo-d and --telo-s. For instance, using --telo-m CCCTAA for human genome assemblies.
3. Integrated --ctg-n to discard too small contigs.

Hifiasm-0.19.8-r603

Since Hifiasm-0.19.7 (r598):

1. Fixed several issues like #461.

Hifiasm-0.19.7-r598

Since Hifiasm-0.19.6 (r595):

1. Incorporated the option --dual-scaf to output scaffoldings.
2. Incorporated the option --scaf-gap to set the max gap size of scaffoldings.

Hifiasm-0.19.6-r595

Since Hifiasm-0.19.5 (r587):

1. Fixed the bugs during the UL integration (#476, #495, #394).
2. Incorporated the option --ul-cut to filter out too short UL reads during the assembly.
3. Incorporated the option --trio-dual to utilize homology information to correct trio phasing errors.

Hifiasm-0.19.5-r587

Since Hifiasm-0.19.4 (r575):

1. Fixed the bug during the UL integration (#441).
2. Based on the Flagger result (https://github.com/mobinasri/flagger), fixed the bugs that the diploid assembly may have false duplications or miss some bases.

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.