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.

YaHS-1.0

This is the first public release of YaHS, a scaffolding tool for HiC data.