Benchmarking of tools for viral haplotype reconstruction.
WARNING: under active construction! May not work as appears, but in such an event feel free to file an issue.
This repo can be used to test a variety of tools and settings to build pipelines for viral haplotype/quasispecies reconstruction on simulated, in vitro and in vivo data.
| Haplotyper | Implemented | Paper | Code |
|---|---|---|---|
| QuasiRecomb | Yes | Link | Link |
| aBayesQR | Yes | Link | Link |
| SAVAGE | Yes | Link | Link |
| RegressHaplo | Yes | Link | Link |
| Haploclique | Yes | Link | Link |
| SHORAH | No | Link | Link |
| PredictHaplo | No | Link | Link |
| QSdpR | No | Link | Link |
| TenSQR | No | Link | Link |
A standard invocation will be of the form:
snakemake output/$DATASET/$QUALITY_CONTROL/$READ_MAPPER/$GENE/$HAPLOTYPER/haplotypes.fasta
where the variables can take one of the following values:
For more information, see the Data section below.
- LANL simulations: see keys of
simulations.jsonfor potential simulation names - Reconstruction: see filenames in
reconstructiondirectory of input data - Evolution: see filenames in
evolutiondirectory of input data - Compartmentalization: see entries in
compartmentalization.jsonin root directory
qfilt, fastp, trimmomatic
bealign, bowtie2, bwa
env, gag, int, nef, pol, pr, prrt, rev, rt, tat, vif, vpr
quasirecomb, abayesqr, savage, regresshaplo
Use of snakemake permits running on TORQUE, i.e.
snakemake --cluster 'qsub -o ./logs -e ./logs -V -d `pwd` -l nodes=1:ppn=$PPN' -j $JOBS -k target
├── compartmentalization
│ ├── $PATIENT_ID/$DATE/$COMPARTMENT/$REPLICATE/reads.fasta
│ ├── $PATIENT_ID/$DATE/$COMPARTMENT/$REPLICATE/scores.qual
├── evolution
│ ├── ERS661087.fastq
│ ├── ERS661088.fastq
│ ├── ERS661089.fastq
│ ├── ERS661090.fastq
│ ├── ERS661091.fastq
│ ├── ERS661092.fastq
│ └── ERS661093.fastq
├── LANL-HIV-aligned.fasta
├── LANL-HIV.fasta
├── LANL-HIV.new
├── README.md
├── reconstruction
│ ├── 3.GAC.454Reads.fna
│ ├── 3.GAC.454Reads.qual
│ ├── 93US141_100k_14-159320-1GN-0_S16_L001_R1_001.fastq
│ ├── 93US141_100k_14-159320-1GN-0_S16_L001_R2_001.fastq
│ ├── BP_050100753.fasta
│ ├── BP_050100753.qual
│ ├── FiveVirusMixIllumina_1.fastq
│ ├── FiveVirusMixIllumina_2.fastq
│ ├── PP1L_S45_L001_R1_001.fastq
│ ├── PP1L_S45_L001_R2_001.fastq
│ ├── regress_haplo.bam
│ ├── regress_haplo.bam.bai
│ ├── sergei1.fastq
│ ├── sergei2.fastq
│ ├── SRR961514-Illumina.sra
│ ├── SRR961596-454.fastq
│ ├── SRR961596-454.sra
│ ├── SRR961669-PacBio.fastq
│ └── SRR961669-PacBio.sra
└── references
├── env.fasta
├── gag.fasta
├── int.fasta
├── nef.fasta
├── pol.fasta
├── pr.fasta
├── prrt.fasta
├── rev.fasta
├── rt.fasta
├── tat.fasta
├── vif.fasta
├── vpr.fasta
└── vpu.fasta
LANL-HIV.fasta
LANL-HIV-aligned.fasta
LANL-HIV.new
HIV genomes from the LANL database, as well as an alignment built with mafft and a tree built with FastTree. Used for simulation.
evolution/ERS6610*.fastq
NGS read data from a study on HIV intra-host evolution.
reconstruction/BP_050100753.fasta
reconstruction/BP_050100753.qual
ACME lab 454 data which shows a clear signal of segregating haplotypes.
reconstruction/SRR961514-Illumina.fastq
reconstruction/SRR961596-454.fastq
reconstruction/SRR961669-PacBio.fastq
A gold standard dataset, consisting of mixed, known strains at known proportions.
reconstruction/sergei1.fastq
reconstruction/sergei2.fastq
A set of paired end reads given by Sergei.
reconstruction/regress_haplo.bam
reconstruction/regress_haplo.bam.bai
Dataset that comes with the RegressHaplo code.
references/*.fasta
HXB2 genes to be used as references when aligning reads.
- Linux (tested on Ubuntu 18.04.1, CentOS 7)
- conda (tested on 4.6.10) with standard BioConda channels
Further requirements listed in environment.yml.
conda env create -f environment.yml
conda activate haplotype-reconstruction