Provides tools and class interfaces for the assembly of DNA reads. AMOS includes modular assembly pipelines, as well as tools for overlapping, consensus generation, contigging, and assembly manipulation. The AMOS pipeline config file can be modified by users to add additional processing steps. The software includes a number of conversion utilities allowing to process data from a variety of input sources and to output the data in commonly used assembly formats.
Integrates the assemblies into a hybrid set of contigs, resulting in assemblies of superior contiguity and accuracy, compared with the assemblies generated by the state-of-the-art assemblers and the hybrid assemblies merged by existing tools. This tool is implemented in Python and requires MUMmer and BLAST+ to be installed on the local machine. A user supplies a set of contigs from at least three assemblers in FASTA format to CISA to obtain integrated contigs.
Allows automation improvement of gene structures in Arabidopsis thaliana. PASA was used in Eukaryotic genome annotation projects such as Rice, Aspergillus species, Plasmodium falciparum, Schistosoma mansoni, Aedes aegypti, mouse, human, among others. This tool is able to recognize and organize splicing variations supported by the transcript alignments. It can clean the transcripts, validate perfect alignments or procced to automatic genome annotation.
Merges two or more assemblies in order to enhance contiguity and correctness of both. GAM-NGS does not rely on global alignment: regions of the two assemblies representing the same genomic locus (called blocks) are identified through reads' alignments and stored in a weighted graph. The merging phase is carried out with the help of this weighted graph that allows an optimal resolution of local problematic regions.
Merges multiple assemblies of a genome into a single superior sequence. We apply it to the four genomes from the Assemblathon competitions and show it consistently and substantially improves the contiguity and quality of each assembly. We also develop guidelines for meta-assembly by systematically evaluating 120 permutations of merging the top 5 assemblies of the first Assemblathon competition.
A hybrid sequencing technology assembler. Zorro merges two sets of pre-assembled contigs into a more contiguous and consistent assembly. The main feature of Zorro is the treatment before and after assembly to avoid errors. Zorro takes 2 contigs fasta files as input (representing assembled contigs from a whole genome assembly) and one fasta file containing some of the reads used for assembly.