NextDenovo2.5.2

Optimize Makefile to adapt to conda build

NextDenovo2.5.1

1. Some small improvements and bugs fixed.

NextDenovo2.5.0

1. Fix a bug about parsing fastq files for HiFi or corrected data, #123 and #119 .
2. Use Paralleltask to submit, control, and monitor jobs.

Re-upload:

• Fixed a typo.

NextDenovo2.4.0

1. Optimized assembly with PacBio HiFi data.
2. Optimized nextgraph speed for ultra-large genomes (>=10 Gb).
3. Optimized the parameter set and added three new parameters: input_type , genome_size and seed_depth.
4. Wrapped the seed_cutoff calculation step into the main pipeline, users do not require to run seq_stat first.
5. Simplified the configuration file, only two parameters (input_fofn and input_type) are required and most parameters can be set automatically.
6. Reformatted the output log information, the log will contain the version number and the parameter set.
7. Fixed a bug that does not output short circular contigs.
8. Added three FAQs, see here for details.
9. Released a compiled version that supports ARM

NextDenovo2.3.1

1. Optimized assembly with PacBio CLR data.
2. Optimized some default parameters for short seed_cutoff.
3. Fixed a bug that seq_stat suggests seed_cutoff is 0.
4. Fixed a memory leak bug in minimap2-nd.
5. Fixed a bug that exits without any errors.
6. Added a function to clip tandem repeats at both end of corrected seeds.
7. Optimized ovl_sort algorithm to produce more high-quality and non-chimeric corrected seeds.
8. Use non-seed reads to correct structural & base errors if seed depth < 35.
9. Changed some default value of some parameters and renamed some parameters of nextgraph.
10. Added limitations and more benchmarks with other assemblers.
11. Some other small improvements and bugs fixed.

NextDenovo2.3.0

1. Added an extra step to correct structural & base errors after the ctg_graph step.
2. Re-constructed the algorithm in nextGraph about removing alternative utgs/bubbles/short branches, which will significantly improve the assembly continuity and accuracy, especially for highly heterozygous genomes.
3. Removed the random_round option.
4. Optimized the CNS algorithm, slightly improved the corrected seed accuracy.
5. Add support for python3
6. Added the assembly quality comparison with Canu, Flye, and Shasta using ONT data from CHM13.
7. Fixed a few of bugs.
8. Lots of other small improvements.

NextDenovo2.2-beta.0

1. Added a fast mode (options: --mode and --cn ) for minimap2-nd, which will be faster for highly repetitive genomes.
2. Improved the CNS accuracy of seeds in highly repetitive or heterozygous regions.
3. Fixed two minor bugs in NextGraph and added a function to break some unexpected connection errors.
4. Added a tutorial about how to configure Drmaa and a function to configure cluster_options automatically.
5. Add a function to assembly from corrected reads without CNS steps.
6. Other small improvements.

NextDenovo2.1-beta.0

1. Fixed a few of bugs.
2. Add a function to del highly repetitive edges.
3. Add an option -G to control whether del potential chimeric edges.
4. Re-construct the function to del low score edges.
5. Increase a better compatibility to run on a slurm system.
6. Add a warning when using the default value of seed_cutoff.
7. Increase more test data to avoid empty results.

NextDenovo2.0-beta.1

1. Reconstruct the error correction algorithm.
2. Initialize NextGraph.
3. Add a more detailed manual.

NextDenovo1.1.1

1. Fix a memory leak bug.