Hifiasm-0.25.0-r726

Since Hifiasm-0.24.0 (r702):

1. For ONT assembly, two new options, --rl-cut and --sc-cut, have been added to internally filter out low-quality reads before assembly.
2. Fixed small-scale misassemblies and improved handling of highly similar repeat copies to prevent their collapse. An example of these errors can be found: #742 (comment). We thanks @kevfengler227 and Sean McKenzie for reporting this issue.

For optimal results with ONT assembly, it is recommended to rerun hifiasm from scratch rather than reusing bin files generated with previous versions of hifiasm.

Hifiasm-0.24.0-r702

Since Hifiasm-0.23.0 (r691):

1. Improved the assembly quality when there are coverage dropouts.

Hifiasm-0.23.0-r691

Since Hifiasm-0.22.0 (r689):

1. Fixed the issue of hifiasm with very high coverage input. This fix applies to all assembly modules, especially for ONT assembly.

Hifiasm-0.22.0-r689

Since Hifiasm-0.21.0 (r686):

1. Fixed the issue that may lead to Segfault (see: #735). This fix applies to all assembly modules.

Known issues:

1. There is a potential issue with hifiasm that has been observed: it may produce suboptimal results when the input data coverage is extremely high. A temporary solution could be down-sampling to 60x by filtering out shorter reads. We aim to solve this issue as soon as possible.

Hifiasm-0.21.0-r686

Since Hifiasm-0.20.0 (r639):

1. New Feature: Introduced a beta module for ONT assembly using ONT simplex R10 reads. To enable this feature, add the --ont option as shown below:

hifiasm -t64 --ont -o ONT.asm ONT.read.fastq.gz

Please note that this beta module requires input reads in FASTQ format.

Hifiasm-0.20.0-r639

This is a relatively large update for hifiasm with the new error correction component. The new error correction component generally allows hifiasm to produce more contiguous genome assemblies with higher quality values (QV) in a shorter amount of time.

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.