Genome assembly Tools

Genomic Mapping and Alignment Program for mRNA and EST Sequences.

GenomeScope2 is a reference-free tool that uses k-mer frequency analysis to estimate genome size, heterozygosity, ploidy, and repeat content from raw sequencing data, supporting both diploid and polyploid genomes.

Genomepy is designed to provide a simple and straightforward way to download and use genomic data. This includes (1) searching available data, (2) showing the available metadata, (3) automatically downloading, preprocessing and matching data and (4) generating optional aligner indexes. All with sensible, yet controllable defaults. Currently, genomepy supports Ensembl, UCSC, NCBI and GENCODE.

The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.

HELEN (Homopolymer Encoded Long-read Error-corrector for Nanopore) is a highly optimized genome polishing pipeline that uses deep learning to correct errors in Nanopore long-read assemblies, working in conjunction with MarginPolish and supporting GPU acceleration for scalability.

Homopolish is a method for the removal of systematic errors in nanopore sequencing by homologous polishing.

KMC is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects.

KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer length which maximizes this number. Experiments show that KmerGenie's choices lead to assemblies that are close to the best possible over all k-mer lengths.

MUMmer4 is an ultrafast genome alignment system for aligning large-scale genomic sequences. It uses suffix trees and maximal unique matches (MUMs) to rapidly find alignments between complete genomes, enabling comparison of closely or distantly related genomes.

Whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454).

MarginPolish is a graph-based assembly polisher. It iteratively finds multiple probable alignment paths for run-length-encoded reads and uses these to generate a refined sequence. It takes as input a FASTA assembly and an indexed BAM (ONT reads aligned to the assembly), and it produces a polished FASTA assembly.

Mauve is a program for performing comaparative analyses of genomes. To generate a new genome alignment with Mauve, select 'Align' from the File menu. To open an existing genome alignment, select 'Open' from the file menu.

MaxBin2 is a software tool for binning assembled metagenomic sequences into individual genomes using an Expectation-Maximization algorithm based on tetranucleotide frequencies and read coverage information, supporting multiple samples simultaneously.

Medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.

Meraculous is a whole genome assembler for Next Generation Sequencing (NGS) data, designed for large genomes. It uses a hybrid k-mer/read-based approach that capitalizes on the high accuracy of Illumina sequencing by eschewing an explicit error correction step, achieving high performance through lightweight data structures and multi-threaded parallelization.

MetaBAT: A robust statistical framework for reconstructing genomes from metagenomic data.

Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.

Get assembly statistics from FASTA and FASTQ files.

An efficient tool for converting genome coordinates between assemblies. CrossMap supports most of the commonly used file formats, including BAM, sequence alignment map, Wiggle, BigWig, browser extensible data, general feature format, gene transfer format and variant call format.

A genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.

Dnaapler is a simple tool that reorients complete circular microbial genomes.

Assemble bacterial isolate genomes from Nanopore reads. Dragonflye is a pipeline that aims to make assembling Oxford Nanopore reads quick and easy.

gfatools is a set of tools for manipulating sequence graphs in the GFA or the rGFA format. It has implemented parsing, subgraph and conversion to FASTA/BED.

khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.

A command-line algorithm for counting k-mers in DNA sequence.

n50 is a simple command-line utility for computing assembly statistics including N50, N90, total length, number of contigs, and other metrics from genome assembly FASTA files.