Hammerhead-View 0.1.3

A tool designed to de novo find potential modification sites.

Hammerhead

This project is designed to find potential modification sites.

Workflow

The Hammerhead was developed specifically to identify potential modification sites using Nanopore R10.4.1 simplex reads. It leverages the strand-specific error pattern observed in these reads to detect modifications.

The pipeline utilizes a self-defined metric called the difference index to quantify the discrepancy in observed accuracy between the forward and reverse strands at individual sites. This difference index serves as a measure of the potential modification probability. A higher value of the difference index indicates a higher likelihood of modification at the corresponding site.

Installation

To use this tool, you'll need to install additional tools or packages for read processing, including samtools and minimap2. The following command can help you install dependencies.

# test verison for dependences
# minimap2	2.17
# samtools	1.17
# bedtools	2.30.0

conda install -c bioconda -c conda-forge minimap2 samtools bedtools

To install this tool, please using the following command.

pip install Hammerhead-View

General usage

Hammerhead can be run using a simple command:

hammerhead --ref <reference> --read <input_fastq>

The help for Hammerhead:

hammerhead -h
usage: hammerhead [-h] --ref  --read  [--cpu] [--cut] [--min_depth] [--min_depth_strand]

A tool help to find the potential modification sites

optional arguments:
  -h, --help           show this help message and exit
  --ref                Input reference (FASTA)
  --read               Input reads (FASTQ)
  --cpu                CPU number. (default:10)
  --cut                Cutoff value [0, 1]. (default:0.35)
  --min_depth          The minimum depth. (default:50)
  --min_depth_strand   The minimum depth for forward strand and reverse strand. (default:25)

Results

The results file for Hammerhead:

├── mapping.mpileup.txt
├── mapping.sort.bam
├── potential_modification_site_detail.bed
├── potential_modification_site_detail.txt
├── enrichment.bed
└── enrichment.fa

• mapping.mpileup.txt - the mpileup file

• mapping.sort.bam - the aligned bam file

• enrichment.bed - the position of sequences around the potential modification sites used for the motif enrichment analysis. (-9 bp, +10 bp)

• enrichment.fa - the sequences around the potential modification sites used for the motif enrichment analysis. (-9 bp, +10 bp)

• potential_modification_site_detail.bed - the position for potential modification sites

• potential_modification_site_detail.txt - the details for potential modification sites

  Chr	Pos	Difference_index	Dif_A	Dif_T	Dif_G	Dif_C	A,T,G,C,a,t,g,c
  contig_2	2541	0.386	0.0	0.386	0.0	0.386	0,2,0,191,0,25,0,38
  contig_2	2836	0.395	0.395	0.0	0.279	0.116	52,0,24,10,129,0,0,0
  contig_2	2837	0.475	0.474	0.029	0.413	0.033	37,1,40,0,0,5,112,4
  

​ A, T, G, C, a, t, g, c is the number of reads mapped as the A/T/G/C in the forward strand and T/A/C/G in the reverse strand.

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