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Addition of README and CHANGELOG
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Delphine-L committed Nov 3, 2023
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# 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.
23 changes: 23 additions & 0 deletions workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/README.md
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# 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

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