Assembly software tools | Shotgun metagenomic sequencing data analysis
Most currently available assemblers were designed to assemble individual genomes or, in some cases, genomes of polyploid eukaryotes; however, they were not designed to assemble metagenomes comprising multiple species with nonuniform sequence coverage, and therefore, their performance with metagenomic data sets varies significantly.
Allows to compare, align, and assemble large sets of DNA sequences. PHRAP uses a banded version of the Smith-Waterman-Gotoh algorithm to do pairwise comparisons of the sequences. It compares sequences by searching for pairs of perfectly matching “words” or sequence regions that meet criteria, tries to extend the alignment if a match of the designated word size is found and then scores it. The software uses quality values produced by the PHRED basecaller. Cross match/Swat is included in the PHRAP package.
Offers a metagenome assembler. MetaVelvet is a four-steps application that: (i) builds a de Bruijn graph; (ii) identifies multiple peaks on k-mer frequency distribution; (iii) splits the constructed de Bruijn graph into individual subgraphs and (iv) assembles contigs and scaffolds. This program can also reconstruct relatively low-coverage genome sequences as scaffolds.
Allows users to perform assembly of large and complex metagenomics next-generation sequencing (NGS) data. MEGAHIT is a standalone software available as both CPU-only and GPU-accelerated versions. It includes five features: (1) general metagenome assembly, (2) a slow and sensitive metagenome assembly, (3) large and complex metagenome assembly, (4) assembly of standard bulk sequencing with sufficient depth and (5) single-cell sequence assembly.
Addresses various challenges of metagenomics assembly by capitalizing on computational ideas that proved to be useful in assemblies of single cells and highly polymorphic diploid genomes. metaSPAdes supports only a single library which has to be paired-end. metaSPAdes assemblies have lower rates of nonunique paired-read alignments, indicating that they are less redundant. metaSPAdes is now released as a part of SPAdes.
Allows metagenomic assembly and analysis. MetAMOS is a modular and customizable framework providing a pushbutton solution for analysis of metagenomic datasets, irrespective of the sequencing technology used. The software integrates many metagenomic analysis tools that can be tailored and extended to meet specific analysis needs. It is built around the features provided by the metagenomic scaffolder Bambus 2.
Allows scaffolding of polymorphic genomes and metagenomes. Bambus implements scaffolding algorithms optimized for non-clonal assembly. When applied to metagenomic datasets, the software generates large scaffolds while avoiding false joins between distantly related organisms. It can automatically identify genomic regions of variation that correspond to previously characterized polymorphic loci. Bambus can be applied to virtually all existing sequencing technologies, and it is sufficient to start with an assembler that is best suited for that type of data.