HAplotype and PHylodynamics pipeline for viral assembly, population genetics, and phylodynamics.
In this User Guide, we assume basic familiarity with conda environments, basic bash knowledge and knowledge of general next-generation sequencing (NGS) concepts. For more information regarding all of these, see helpful links and FAQ. Remember that a directory is a simply a folder nesting system, similar to what you see on your computer. Where you see "folder" below you can also say "directory."
HAPHPIPE is intended only for Linux and Mac OS X platforms. If you are a Windows user, see this section on our install page.
This User Guide was developed jointly by undergraduate and graduate students to be accessible for users at all stages. Margaret C. Steiner, Keylie M. Gibson, Matthew L. Bendall, Uzma Rentia, and Pengfei Li all contributed to developing this User Guide and testing HAPHPIPE.
See our protocol paper (link coming soon) for more information and this paper for our validation study.
When using HAPHPIPE, please cite our article when it is available. For now, reference the GitHub website: https://github.com/gwcbi/haphpipe and the validation paper.
The HAPHPIPE suite
Each stage can be run on its own. Stages are grouped into 4 categories:
More detailed description of command line options for each stage are available in the below sections. To view all available stages in HAPHPIPE, run:
Output will look like:
Program: haphpipe (haplotype and phylodynamics pipeline) Version: 1.0.2 Commands: -- Reads sample_reads subsample reads using seqtk trim_reads trim reads using Trimmomatic join_reads join reads using FLASh ec_reads error correct reads using SPAdes -- Assemble assemble_denovo assemble reads denovo assemble_amplicons assemble contigs to amplicon regions assemble_scaffold assemble contigs to genome align_reads align reads to reference call_variants call variants vcf_to_consensus create consensus sequence from VCF refine_assembly iterative refinement: align - variants - consensus finalize_assembly finalize consensus sequence -- Haplotype predict_haplo assemble haplotypes with PredictHaplo ph_parser parse output from PredictHaplo cliquesnv assemble haplotypes with CliqueSNV -- Description pairwise_align align consensus to an annotated reference extract_pairwise extract sequence regions from pairwise alignment summary_stats generates summary statistics for samples -- Phylo multiple_align multiple sequence alignment model_test tests for model of evolution using ModelTest build_tree_NG builds phylogenetic tree with RAxML-NG -- Miscellaneous demo setup demo directory and test data
HAPHPIPE consists of a suite of sub-commands under each stage that are invoked as follows:
haphpipe [stage] [sub-command] [options]
For example, to join paired end reads, one would invoke the following:
haphpipe join_reads --fq1 trimmed_1.fastq --fq2 trimmed_2.fastq