YaHS-1.2.2

This release addresses a bug in juicer post introduced in version 1.2.1. Version 1.2 and earlier are unaffected.

No new features are included in this release. The scaffolding results should be consistent with those from version 1.2 and 1.2.1.

A script has been added to facilitate installation testing. To run the test, use the command make test or execute bash scripts/run_test.sh.

YaHS-1.2.1

Now YaHS supports gzipped BED and PA5 file input.

This release also fixed a few bugs that may cause segfaults when scaffolding failed to run.

YaHS-1.2

Major changes in this release.

1. Improved compatibility with AGP specifications. The default component type is now 'U' (previously 'N'). The default gap size is now 100 (previously 200). The default linkage evidence is now 'proximity_ligation' ( previously 'na'). These defaults can be adjusted using parameters '--gap-ctype', '--gap-size' and '--gap-link', respectively. For more details, refer to the full help message by running yahs -?.

2. The scaffolding logic has been updated. In previous versions, the scaffolding process would stop if the N50 was too small for a given resolution. Now, the process will attempt additional rounds of scaffolding at the previous resolution level and will only terminate if there are still no significant improvements.

3. A new '-R' option has been added to control the number of rounds to run at each resolution level.

4. The behavior of the '-a' option has been changed. In previous versions, when an AGP file was provided for rescaffolding, contig error correction was not performed by default. Now, contig error correction is enabled by default.

5. A telomeric sequence identification module has been integrated to detect chromosome ends. Sequences identified as telomeric will be prevented from joining other sequences. YaHS includes a default telomeric motif database (you can view the list by running yahs --print-telo-motifs). The --telo-motif option can be used to specify a custom telomeric motif. When this option is set, only the specified motif will be checked. The code for telomere identification was adopted from seqtk telo.

YaHS-1.2a.1.patch

Change juicer exit code for bioconda recipe. No feature changes.

YaHS-1.2a.1

Add the option --no-mem-check to allow disabling of runtime memory check.

YaHS-1.2a

In this release, the mapping quality score is added to the binary file, which makes the BIN files generated with the previous versions not compatible anymore. If you see error messages indicating the BIN file is not valid, you need to run YaHS with a BED or BAM file to regenerate a BIN file.

This change mainly aims to reduce false-positive contig breaks in repetitive regions. When mapping quality filtering is applied, the HiC coverage in these regions is usually low, leading to excessive contig breaks. It is therefore highly recommended to keep low mapping quality reads in the YaHS input file. All the reads will be used in the contig error detection stage. In the scaffolding stage, the parameter -q (10 by default) is applied to select valid read pairs.

YaHS-1.1

This release is to support manual curation with JuiceBox and also includes some bug fixes.

YaHS-1.1a.2

OSX compatibility for a bioconda recipe

YaHS-1.1a.1

Pre-release for version 1.1. Bug fix for BAM input processing. Support for >4G scaffolds. Experimental implementation for restriction enzymes.

YaHS-1.1a

Pre-release for version 1.1. Bug fix and new strategies for scaffolding graph pruning. This version should be more reliable in dealing with high-level background noise.