Quick start

    tandemquast.py --nano test_data/simulated_reads.fasta test_data/simulated_polished.fa -o simulated_res

Introduction

TandemTools package includes TandemQUAST tool for evaluating and improving assemblies of extra-long tandem repeats (ETR) and TandemMapper tool for mapping long error-prone reads to ETRs.

Note: TandemTools is designed specifically for ETR (range in length from hundreds of thousands to millions of nucleotides). It is strongly not recommended to run TandemTools on shorter TRs.

Installation

Requirements are listed in requirements.txt and can be installed through Conda as conda install --file requirements.txt.

Usage

tandemquast.py [options] --nano/--pacbio <reads_file> -o <output_dir> <assembly_file1> <assembly_file2>

Required arguments:
    --nano         PATH                 File with Oxford Nanopore reads used for ETR assembly 
      or
    --pacbio       PATH                 File with PacBio CLR reads used for ETR assembly
    -o             PATH                 Folder to store all result files

Optional arguments:    
    -t             INT                  Maximum number of threads [default: 4]
    -l             \"label,label,...\"  Human-readable names of assemblies to use in reports, comma-separated. If contain spaces, use quotes 
    -m             PATH                 FASTA file with monomer sequences
    --hifi         PATH                 File with accurate PacBio HiFi reads
    --only-polish                       Run tandemQUAST polishing module (metrics will not be calculated).

tandemmapper.py [options] --nano/--pacbio <reads_file> -o <output_dir> <assembly_file1> <assembly_file2>

Required arguments:
    --nano         PATH                 File with Oxford Nanopore reads used for ETR assembly 
      or
    --pacbio       PATH                 File with PacBio CLR reads used for ETR assembly
    -o             PATH                 Folder to store alignment results

Optional arguments:    
    -t             INT                  Maximum number of threads [default: 4]

Output files

The following files are contained in <output_dir> directory (specified by -o) and include results for all input assemblies. See TandemQUAST paper for the detailed explanation of different metrics.

TandemMapper output

<output_dir>/*_alignment.bed - TandemMapper alignments in BED format

<output_dir>/*_alignment.sam - TandemMapper alignments in SAM format

TandemQUAST output

Basic metrics:

<output_dir>/report/*_coverage.png - plot of read coverage.

<output_dir>/report/*_bp_analysis.png - plot of breakpoint ratio values (see TandemQUAST paper for the details). The red peaks in this plot may correspond to large-scale assembly errors.

<output_dir>/report/*_kmer_analysis.png - distribution of different types of unique k-mers along the assembly. Each bar shows the number of different types of k-mers in a bin of length 20 kb. The blue bars represent single-clump k-mers. The high number of single-clump k-mers suggests the good base-level quality of the assembly. The orange (multiple-clumps) and green (no-clumps) bars suggest a low base-level quality in the region, caused by lack of polishing or an assembly error.

<output_dir>/report/*_kmer_stats.txt - distribution of different types of unique k-mers in TXT format.

Pairwise comparison:

<output_dir>/report/*_vs_*.png - a dot plot comparing mappings for two assemblies

<output_dir>/report/discordance_*_vs_*.png - a discordance plot showing coverage of two assemblies by discordant reads. The peaks of coverage for one assembly suggest that this assembly is more "supported" by reads in this region than other assembly.

Centromeric metrics:

<output_dir>/report/*_monomer_lengths.html - an interactive HTML-page showing monomer length distribution along the assembly.

<output_dir>/report/*_units.txt - file with a list of HOR units.

Citation

Alla Mikheenko, Andrey V. Bzikadze, Alexey Gurevich, Karen H. Miga, and Pavel A. Pevzner. TandemMapper and TandemQUAST: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats, 2019, bioRxiv

Contacts

Please report any problems to the issue tracker. Alternatively, you can write directly to [email protected].