diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md new file mode 100644 index 000000000..92bf39f8e --- /dev/null +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md @@ -0,0 +1,12 @@ +# Changelog + +All notable changes to this project will be documented in this file. + +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), +and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +## [Unreleased] + +## [0.1] - 2023-09-27 + +Creation of workflow for HiFi assembly with Hi-C phasing. diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/README.md b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/README.md new file mode 100644 index 000000000..1cc40e5db --- /dev/null +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/README.md @@ -0,0 +1,23 @@ +# Contiging Solo w/HiC: + +Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing. + +## Inputs + +1. Hifi long reads [fastq] +2. HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq] +3. HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq] +4. K-mer database [meryldb] +5. Genome profile summary generated by Genomescope [txt] +6. Name of first assembly +7. Name of second assembly + +## Outputs + +1. Haplotype 1 assembly ([fasta] and [gfa]) +2. Haplotype 2 assembly ([fasta] and [gfa]) +3. QC: BUSCO report for both assemblies +4. QC: Merqury report for both assemblies +5. QC: Assembly statistics for both assemblies +6. QC: Nx plot for both assemblies +7. QC: Size plot for both assemblies \ No newline at end of file