HapHiC

https://github.com/zengxiaofei/haphic
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HapHiC is a fast, reference-independent scaffolding tool that uses Hi-C data to assemble...
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### Install HapHiC and Dependencies via Conda

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

This code snippet demonstrates how to clone the HapHiC repository from GitHub, create a Conda environment with all necessary dependencies, and activate it. It also includes a command to check if the dependencies were installed correctly.

```bash
# (1) Download HapHiC from GitHub
$ git clone https://github.com/zengxiaofei/HapHiC.git

# (2) Resolve dependencies
# We strongly recommend using conda to install dependencies. If you prefer manual installation, refer to HapHiC/conda_env/create_conda_env_py310.sh
# We have also included additional environments for Python 3.11 and 3.12 in the directory HapHiC/conda_env/
$ conda env create -f HapHiC/conda_env/environment_py310.yml
# Activate the HapHiC conda environment
$ conda activate haphic # or: source /path/to/conda/bin/activate haphic

# (3) Check whether all dependencies are correctly installed
$ /path/to/HapHiC/haphic check
```

--------------------------------

### Install HapHiC via Conda Environment

Source: https://context7.com/zengxiaofei/haphic/llms.txt

Installs HapHiC and its dependencies using a provided conda environment file. Requires Git to clone the repository and Conda for environment management. Verifies installation by running the 'haphic check' command.

```bash
# Clone the repository
git clone https://github.com/zengxiaofei/HapHiC.git

# Create conda environment with all dependencies
conda env create -f HapHiC/conda_env/environment_py310.yml

# Activate the environment
conda activate haphic

# Verify installation
/path/to/HapHiC/haphic check
```

--------------------------------

### Execute Juicebox Visualization Script

Source: https://context7.com/zengxiaofei/haphic/llms.txt

Runs the auto-generated Juicebox visualization script to generate files for manual curation in Juicebox. This requires Java and samtools to be installed on the system.

```bash
bash juicebox.sh
```

--------------------------------

### Generate Final FASTA from Curated Assembly

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Generates the final FASTA file for scaffolds after manual curation in Juicebox. Requires Java and samtools to be installed and in the PATH. It takes the curated assembly file and an AGP file as input.

```bash
# Generate the final FASTA file for the scaffolds
$ /path/to/HapHiC/utils/juicer post -o out_JBAT out_JBAT.review.assembly out_JBAT.liftover.agp asm.fa
```

--------------------------------

### Run Juicebox Visualization Script

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Executes a shell script generated by HapHiC for visualizing and curating Hi-C data in Juicebox. Requires Java to be installed and in the PATH. Adjustments to Java memory settings may be needed for large genomes.

```bash
# bash, not sh
$ bash juicebox.sh
```

--------------------------------

### Optimize HapHiC Pipeline Performance

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

This command demonstrates how to optimize the HapHiC pipeline's performance by specifying the number of threads for BAM file reading and the number of processes for contig ordering and orientation. It uses the `--threads` and `--processes` parameters, both set to 8 in this example.

```bash
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam nchrs --threads 8 --processes 8
```

--------------------------------

### Generate AGP File for FASTA

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Creates a mock AGP file for a given chromosome-level FASTA file. This is a utility script to prepare AGP files for visualization with 'haphic plot' when starting from a FASTA file.

```bash
# This script generates an AGP file for your FASTA file
$ /path/to/HapHiC/utils/mock_agp_file.py chr_asm.fa > chr_asm.agp
```

--------------------------------

### Align Hi-C Data using BWA and Samblaster

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Aligns Hi-C reads to a reference assembly using BWA, removes PCR duplicates with Samblaster, and filters alignments using samtools. Requires BWA, Samblaster, and Samtools to be installed.

```bash
bwa index asm.fa
bwa mem -5SP -t 28 asm.fa /path/to/read1_fq.gz /path/to/read2_fq.gz | samblaster | samtools view - -@ 14 -S -h -b -F 3340 -o HiC.bam
```

--------------------------------

### Run HapHiC Scaffolding Pipeline (Default)

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Executes the complete HapHiC scaffolding pipeline with default settings. Requires the genome assembly FASTA file, a filtered BAM file, and the number of chromosomes.

```bash
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam nchrs
```

--------------------------------

### Show HapHiC Help Message

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Displays all available commands and the general help message for the HapHiC tool. This is useful for understanding the tool's capabilities and options.

```bash
/path/to/HapHiC/haphic -h
```

--------------------------------

### Run HapHiC Pipeline in Quick View Mode

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Enables quick view mode in HapHiC, which orders and orients all contigs without clustering. This mode is useful when the exact chromosome count is unknown or for a rapid assembly overview. It supports correcting input contigs and partitioning haplotypes using GFA files.

```bash
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam nchrs --quick_view

```

```bash
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam nchrs --quick_view --correct_nrounds 2

```

```bash
/path/to/HapHiC/haphic pipeline allhaps.fa HiC.filtered.bam nchrs --quick_view --gfa "hap1.p_ctg.gfa,hap2.p_ctg.gfa"

```

--------------------------------

### HapHiC Juicer Command

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

A simplified command to initiate the HapHiC juicer process, likely for preparing data for Juicebox visualization or curation.

```bash
/path/to/HapHiC/haphic juicer

```

--------------------------------

### HapHiC Clustering with MCL Algorithm

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Performs initial contig clustering using the Markov Cluster (MCL) algorithm. This step involves preprocessing, filtering, and then clustering contigs based on Hi-C links. The 'inflation' parameter controls the granularity of clusters. Outputs include corrected assemblies, link files, and intermediate cluster results for various inflation values.

```bash
/path/to/HapHiC/haphic cluster asm.fa HiC.filtered.bam nchrs
```

--------------------------------

### Generate Final FASTA from Curated Assembly

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Converts a manually curated assembly file (scaffolds.review.assembly) back into a FASTA format. This script is used after manual curation in Juicebox to obtain the final scaffold sequences.

```bash
/path/to/juicebox_scripts/juicebox_assembly_converter.py -a scaffolds.review.assembly -f asm.fa -s

```

--------------------------------

### Run HapHiC Scaffolding Pipeline with Custom Restriction Site

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Runs the HapHiC scaffolding pipeline specifying a custom restriction enzyme site for Hi-C library preparation. Use the --RE parameter followed by the enzyme's recognition sequence.

```bash
# For HindIII
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam nchrs --RE "AAGCTT"
# For Arima two-enzyme chemistry
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam nchrs --RE "GATC,GANTC"
# For Arima four-enzyme chemistry
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam nchrs --RE "GATC,GANTC,CTNAG,TTAA"
```

--------------------------------

### Run HapHiC One-Line Scaffolding Pipeline

Source: https://context7.com/zengxiaofei/haphic/llms.txt

Executes the complete HapHiC scaffolding pipeline with various options for restriction enzymes, assembly correction, and allelic link removal. Takes assembly FASTA and filtered BAM as input, along with the expected chromosome count. Outputs include AGP files, FASTA scaffolds, and a visualization script.

```bash
# Basic usage with MboI/DpnII restriction enzyme (GATC)
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam 10

# For HindIII restriction enzyme
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam 10 --RE "AAGCTT"

# For Arima two-enzyme chemistry
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam 10 --RE "GATC,GANTC"

# Enable assembly correction (2 rounds)
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam 10 --correct_nrounds 2

# Remove allelic links for phased tetraploid assembly
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam 40 --remove_allelic_links 4

# Optimize performance with multiple threads and processes
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam 10 --threads 8 --processes 8
```

--------------------------------

### Perform HapHiC Step-by-Step Clustering

Source: https://context7.com/zengxiaofei/haphic/llms.txt

Executes the Markov clustering step of HapHiC for grouping contigs into chromosomes. Supports assembly correction and adjustable inflation parameters for clustering. Requires assembly FASTA, filtered BAM, and expected chromosome count. Outputs clustering results and logs.

```bash
# Basic clustering with automatic inflation parameter selection
/path/to/HapHiC/haphic cluster asm.fa HiC.filtered.bam 10

# Enable assembly correction before clustering
/path/to/HapHiC/haphic cluster asm.fa HiC.filtered.bam 10 --correct_nrounds 2

# Adjust clustering parameters
/path/to/HapHiC/haphic cluster asm.fa HiC.filtered.bam 10 \
  --min_inflation 1.0 \
  --max_inflation 5.0 \
  --inflation_step 0.2

# Remove allelic links for better phased assembly clustering
/path/to/HapHiC/haphic cluster asm.fa HiC.filtered.bam 20 --remove_allelic_links 2
```

--------------------------------

### Post-processing and FASTA Generation with Juicebox

Source: https://context7.com/zengxiaofei/haphic/llms.txt

Generates final FASTA files after manual curation in Juicebox. This process uses the `juicer post` command to create assembly files and the final FASTA output. Ensure sufficient Java memory is allocated for large genomes.

```bash
#!/bin/bash
# After manual curation in Juicebox, generate final FASTA
/path/to/HapHiC/utils/juicer post -o out_JBAT \
  out_JBAT.review.assembly \
  out_JBAT.liftover.agp \
  asm.fa
```

--------------------------------

### Hi-C Contact Map Visualization with HapHiC Plot

Source: https://context7.com/zengxiaofei/haphic/llms.txt

Creates publication-quality Hi-C contact maps for visualizing genome assembly. Supports plotting from AGP files and BAM files, or pre-computed matrices for faster visualization. Options allow customization of bin size, minimum scaffold length, colormap, and normalization.

```bash
# Basic contact map visualization
/path/to/HapHiC/haphic plot scaffolds.raw.agp HiC.filtered.bam

# Visualize manually curated assembly
/path/to/HapHiC/haphic plot out_JBAT.FINAL.agp HiC.filtered.bam

# Use pre-computed matrix for faster visualization
/path/to/HapHiC/haphic plot out_JBAT.FINAL.agp contact_matrix.pkl

# Customize bin size and minimum scaffold length
/path/to/HapHiC/haphic plot out_JBAT.FINAL.agp HiC.filtered.bam \
  --bin_size 1000 \
  --min_len 5

# Generate separate plots for each scaffold
/path/to/HapHiC/haphic plot out_JBAT.FINAL.agp HiC.filtered.bam --separate_plots

# Customize colormap and normalization
/path/to/HapHiC/haphic plot out_JBAT.FINAL.agp contact_matrix.pkl \
  --colormap "Reds" \
  --normalize "log" \
  --origin "lower"
```

--------------------------------

### HapHiC Scaffolding with Hifiasm Primary Unitigs (Bash)

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

This command demonstrates how to use HapHiC to scaffold primary unitigs from hifiasm. It leverages read depth information within the GFA file to filter collapsed unitigs prior to clustering. The input includes a FASTA file of primary unitigs, a filtered Hi-C BAM file, the number of chromosomes, and the GFA file.

```bash
# (1) For hifiasm primary unitigs (`*.p_utg.gfa`), use the read depth informtion in the GFA file to filter out potential collapsed unitigs before clustering
$ /path/to/HapHiC/haphic pipeline p_utg.fa HiC.filtered.bam nchrs --gfa p_utg.gfa
```

--------------------------------

### HapHiC Build Final Scaffolds

Source: https://context7.com/zengxiaofei/haphic/llms.txt

Generates chromosome-scale scaffolds from tour files. This command takes assembly sequences, Hi-C data, and tour files to construct scaffolds. It can incorporate assembly correction information and sort scaffolds according to a reference genome order. The output includes AGP files, FASTA sequences, and a Juicebox visualization script.

```bash
# Build scaffolds without assembly correction
/path/to/HapHiC/haphic build asm.fa asm.fa HiC.filtered.bam final_tours/group*.tour
```

```bash
# Build scaffolds with assembly correction
/path/to/HapHiC/haphic build corrected_asm.fa asm.fa HiC.filtered.bam \
  final_tours/group*.tour --corrected_ctgs corrected_ctgs.txt
```

```bash
# Sort scaffolds by reference genome order
/path/to/HapHiC/haphic build corrected_asm.fa asm.fa HiC.filtered.bam \
  final_tours/group*.tour \
  --corrected_ctgs corrected_ctgs.txt \
  --ref_order "chr1,chr2,chr3,chr4,chr5"
```

--------------------------------

### Visualize Hi-C Contact Maps with HapHiC

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Generates customizable Hi-C contact maps using the 'haphic plot' command. Requires a filtered BAM file and a scaffold AGP file. The visualization can be accelerated by using a pre-generated binary contact matrix file.

```bash
# For HapHiC scaffolding result
$ /path/to/HapHiC/haphic plot scaffolds.raw.agp HiC.filtered.bam
# For the AGP file generated after manual curation in Juicebox
$ /path/to/HapHiC/haphic plot out_JBAT.FINAL.agp HiC.filtered.bam
# Use previously generated `contact_matrix.pkl` for faster visualization
$ /path/to/HapHiC/haphic plot out_JBAT.FINAL.agp contact_matrix.pkl
```

--------------------------------

### HapHiC Contig Ordering and Orientation

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Orders and orients contigs using an integration of 3D-DNA and ALLHiC algorithms. It takes the assembly FASTA, clustering output, split contig information, and group files as input. The `--processes` parameter controls parallel execution. The output includes tour files detailing contig ordering and orientation within groups.

```bash
/path/to/HapHiC/haphic sort asm.fa HT_links.pkl split_clms final_groups/group*.txt --processes 8
```

--------------------------------

### HapHiC Quick View Mode for Rapid Scaffolding

Source: https://context7.com/zengxiaofei/haphic/llms.txt

Generates rapid scaffolding results without clustering, suitable for unknown chromosome numbers or failed clustering. This mode orders and orients all contigs directly. It can be used with or without assembly correction and supports haplotype partitioning.

```bash
# Quick view for unknown chromosome number
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam 1 --quick_view
```

```bash
# Quick view with assembly correction
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam 1 \
  --quick_view \
  --correct_nrounds 2
```

```bash
# Quick view with haplotype partitioning
/path/to/HapHiC/haphic pipeline allhaps.fa HiC.filtered.bam 1 \
  --quick_view \
  --gfa "hap1.p_ctg.gfa,hap2.p_ctg.gfa"
```

--------------------------------

### HapHiC Scaffolding with Hifiasm Haplotype-Resolved Contigs (Bash)

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

This command showcases HapHiC's capability to scaffold haplotype-resolved primary contigs from hifiasm. Beyond read depth filtering, it can also reduce Hi-C links between haplotypes based on phasing information present in the GFA files. This aids in accurate haplotype phasing during the clustering process.

```bash
# (2) In addition to read depth filtering, HapHiC can also reduce Hi-C links between haplotypes according to phasing information in GFA files for haplotype-resolved primary contigs (`*.hap*.p_ctg.gfa`)
```

--------------------------------

### Run HapHiC Scaffolding Pipeline with Contig Correction

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Enables and configures assembly correction rounds within the HapHiC scaffolding pipeline. Use --correct_nrounds to specify the number of correction passes, typically two.

```bash
# Typically, two rounds of assembly correction are enough
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam nchrs --correct_nrounds 2
```

--------------------------------

### HapHiC Scaffold Building (With Correction)

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Builds final scaffolds when assembly correction has been performed. It uses the corrected assembly FASTA, the original assembly FASTA, HiC data, tour files, and a file specifying corrected contigs. The `--corrected_ctgs` parameter is crucial for accurate scaffold generation. Outputs include AGP files and final FASTA scaffolds.

```bash
/path/to/HapHiC/haphic build corrected_asm.fa asm.fa HiC.filtered.bam final_tours/group*.tour --corrected_ctgs corrected_ctgs.txt
```

--------------------------------

### Run HapHiC Pipeline for Autotetraploids

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

This command executes the HapHiC pipeline for haplotype-phased assemblies of autotetraploids. It sets the `--remove_allelic_links` parameter to 4, which is recommended for such assemblies. The command takes the assembly FASTA file and the filtered Hi-C BAM file as input, along with the 'nchrs' argument.

```bash
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam nchrs --remove_allelic_links 4
```

--------------------------------

### Run HapHiC Pipeline with Phasing

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Executes the HapHiC pipeline to remove Hi-C links between haplotypes. It uses contigs and a filtered BAM file, optionally incorporating phasing information from GFA files. The --phasing_weight parameter controls the influence of phasing confidence.

```bash
/path/to/HapHiC/haphic pipeline allhaps.fa HiC.filtered.bam nchrs --gfa "hap1.p_ctg.gfa,hap2.p_ctg.gfa"

```

```bash
/path/to/HapHiC/haphic pipeline allhaps.fa HiC.filtered.bam nchrs --gfa "hap1.p_ctg.gfa,hap2.p_ctg.gfa" --phasing_weight 0

```

--------------------------------

### HapHiC Scaffold Building (No Correction)

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Builds final scaffolds (pseudomolecules) using contig assignment, ordering, and orientation information. This command is used when assembly correction has not been performed. It requires the assembly FASTA, HiC data, and tour files as input. The output includes AGP files and the final FASTA scaffolds.

```bash
/path/to/HapHiC/haphic build asm.fa asm.fa HiC.filtered.bam final_tours/group*.tour
```

--------------------------------

### Juicebox Curation: SALSA-style AGP

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Generates .assembly and .hic files for Juicebox visualization using a SALSA-style AGP. This involves generating an .mnd file with matlock, converting AGP to assembly format, and then creating the .hic file using 3D-DNA's run-assembly-visualizer.sh. This method is not recommended if contigs were corrected by HapHiC.

```bash
/path/to/matlock bam2 juicer HiC.filtered.bam out.links.mnd
sort -k2,2 -k6,6 out.links.mnd > out.sorted.links.mnd

```

```bash
/path/to/juicebox_scripts/agp2assembly.py scaffolds.agp scaffolds.assembly

```

```bash
bash /path/to/3d-dna/visualize/run-assembly-visualizer.sh -p false scaffolds.assembly out.sorted.links.mnd

```

--------------------------------

### Align Hi-C Reads and Filter BAM

Source: https://context7.com/zengxiaofei/haphic/llms.txt

Performs Hi-C read alignment using BWA, removes PCR duplicates with Samblaster, and filters alignments based on MAPQ and edit distance using samtools and HapHiC's filter_bam utility. The resulting BAM file must be sorted by read name. Inputs include assembly FASTA and paired-end FASTQ files.

```bash
# Index the assembly
bwa index asm.fa

# Align Hi-C data, remove PCR duplicates, filter secondary/supplementary alignments
bwa mem -5SP -t 28 asm.fa read1.fq.gz read2.fq.gz | \
  samblaster | \
  samtools view -@ 14 -S -h -b -F 3340 -o HiC.bam

# Filter alignments with MAPQ >= 1 and edit distance < 3
/path/to/HapHiC/utils/filter_bam HiC.bam 1 --nm 3 --threads 14 | \
  samtools view -b -@ 14 -o HiC.filtered.bam
```

--------------------------------

### Customize HapHiC Contact Map Visualization

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Allows customization of Hi-C contact map generation parameters such as bin size, minimum scaffold length, and whether to generate separate plots per scaffold. Uses the 'haphic plot' command with additional arguments.

```bash
# Set the bin size to 1 Mbp and display only scaffolds longer than 5 Mbp
$ /path/to/HapHiC/haphic plot out_JBAT.FINAL.agp HiC.filtered.bam --bin_size 1000 --min_len 5
# Create separate plots for each scaffold
$ /path/to/HapHiC/haphic plot out_JBAT.FINAL.agp HiC.filtered.bam --separate_plots
```

--------------------------------

### HapHiC Pipeline for Hifiasm Assemblies

Source: https://context7.com/zengxiaofei/haphic/llms.txt

Scaffolds assemblies using Hifiasm phasing information, leveraging GFA read depth for filtering and potentially reducing Hi-C links between haplotypes. It can process phased unitigs or haplotype-resolved contigs. Parameters control phasing confidence and enable quick view mode.

```bash
# Scaffold phased unitigs with read depth filtering
/path/to/HapHiC/haphic pipeline p_utg.fa HiC.filtered.bam 10 --gfa p_utg.gfa
```

```bash
# Scaffold haplotype-resolved contigs with phasing information
/path/to/HapHiC/haphic pipeline allhaps.fa HiC.filtered.bam 20 \
  --gfa "hap1.p_ctg.gfa,hap2.p_ctg.gfa"
```

```bash
# Adjust phasing confidence level (0=ignore phasing, 1=full confidence)
/path/to/HapHiC/haphic pipeline allhaps.fa HiC.filtered.bam 20 \
  --gfa "hap1.p_ctg.gfa,hap2.p_ctg.gfa" \
  --phasing_weight 0.5
```

```bash
# Quick view mode with haplotype partitioning
/path/to/HapHiC/haphic pipeline allhaps.fa HiC.filtered.bam 20 \
  --quick_view \
  --gfa "hap1.p_ctg.gfa,hap2.p_ctg.gfa"
```

--------------------------------

### HapHiC Sort Contigs for Ordering and Orientation

Source: https://context7.com/zengxiaofei/haphic/llms.txt

Orders and orients contigs within each chromosome group. This step utilizes Hi-C links and group information to determine the sequence of contigs. It supports parallel processing and can be configured to skip fast sorting or adjust ALLHiC optimization time. The output includes tour files and final tour files.

```bash
# Basic sorting with 8 parallel processes
/path/to/HapHiC/haphic sort corrected_asm.fa HT_links.pkl split_clms \
  final_groups/group*.txt --processes 8
```

```bash
# Use ALLHiC optimization only (skip fast sorting)
/path/to/HapHiC/haphic sort corrected_asm.fa HT_links.pkl split_clms \
  final_groups/group*.txt \
  --processes 8 \
  --skip_allhic False \
  --skip_fast_sorting True
```

```bash
# Adjust optimization parameters
/path/to/HapHiC/haphic sort corrected_asm.fa HT_links.pkl split_clms \
  final_groups/group*.txt \
  --processes 8 \
  --allhic_optimize_time 18000
```

--------------------------------

### Reference-Based Scaffold Reordering with HapHiC Refsort

Source: https://context7.com/zengxiaofei/haphic/llms.txt

Reorders and reorients scaffolds using a reference genome. This involves aligning contigs to the reference using minimap2 and then using `haphic refsort` to generate a new AGP file. Options allow specifying custom chromosome order, generating a FASTA file, and keeping original scaffold IDs.

```bash
# Align contigs to reference genome
minimap2 -x asm20 ref.fa asm.fa --secondary=no -t 28 -o asm_to_ref.paf

# Reorder scaffolds alphabetically by reference chromosome IDs
haphic refsort scaffolds.raw.agp asm_to_ref.paf > scaffolds.refsort.agp

# Specify custom chromosome order
haphic refsort scaffolds.raw.agp asm_to_ref.paf \
  --ref_order "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10" \
  > scaffolds.refsort.agp

# Generate reordered FASTA file
haphic refsort scaffolds.raw.agp asm_to_ref.paf \
  --fasta asm.fa \
  > scaffolds.refsort.agp

# Keep original scaffold IDs instead of renaming
haphic refsort scaffolds.raw.agp asm_to_ref.paf \
  --keep_original_ids \
  --fasta asm.fa \
  > scaffolds.refsort.agp
```

--------------------------------

### Run HapHiC Scaffolding Pipeline to Remove Allelic Links

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Removes Hi-C links between allelic contigs to improve scaffolding in haplotype-phased assemblies with high switch error rates. Use --remove_allelic_links with the ploidy value.

```bash
# Example for diploid assembly
/path/to/HapHiC/haphic pipeline asm.fa HiC.filtered.bam nchrs --remove_allelic_links 2
```

--------------------------------

### HapHiC Reassignment for Cluster Refinement

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Refines and corrects contig assignments after initial clustering. This step rescues unassigned contigs, reassigns mis-clustered contigs, and uses agglomerative hierarchical clustering to merge groups if necessary, ensuring the final number of clusters matches the specified number of chromosomes. Requires outputs from the clustering step.

```bash
/path/to/HapHiC/haphic reassign asm.fa full_links.pkl mcl_inflation_x.clusters.txt paired_links.clm --nclusters nchrs
```

--------------------------------

### HapHiC Reassign Contigs with Clustering Output

Source: https://context7.com/zengxiaofei/haphic/llms.txt

Reassigns contigs based on clustering output from MCL. This step uses the corrected assembly, full Hi-C links, and cluster information to group contigs. It outputs group-specific files and split CLM directories for the next stage. Key parameters include the number of clusters.

```bash
/path/to/HapHiC/haphic reassign corrected_asm.fa full_links.pkl \
  mcl_inflation_2.5.clusters.txt paired_links.clm --nclusters 10
```

```bash
# Adjust anchoring parameters for higher anchoring rate
/path/to/HapHiC/haphic reassign corrected_asm.fa full_links.pkl \
  mcl_inflation_2.5.clusters.txt paired_links.clm \
  --nclusters 10 \
  --min_RE_sites 15 \
  --min_links 15 \
  --min_link_density 0.00005
```

```bash
# For small genomes, adjust filtering parameters
/path/to/HapHiC/haphic reassign corrected_asm.fa full_links.pkl \
  mcl_inflation_2.5.clusters.txt paired_links.clm \
  --nclusters 10 \
  --min_group_len 0
```

--------------------------------

### Filter BAM Alignments with MAPQ and Edit Distance

Source: https://github.com/zengxiaofei/haphic/blob/main/README.md

Filters a BAM file based on mapping quality (MAPQ) and edit distance (NM). This step refines the alignment data for subsequent scaffolding. Requires the HapHiC utility script 'filter_bam' and samtools.

```bash
/path/to/HapHiC/utils/filter_bam HiC.bam 1 --nm 3 --threads 14 | samtools view - -b -@ 14 -o HiC.filtered.bam
```
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