AMOS: A Modular Open-Source Assembler
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IDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics. Most assemblers based on de Bruijn graph build a de Bruijn graph with a specific k to perform the assembling task. For all of them, it is very crucial to find a specific value of k. If k is too large, there will be a lot of gap problems in the graph. If k is too small, there will a lot of branch problems. IDBA uses not only one specific k but a range of k values to build the iterative de Bruijn graph. It can keep all the information in graphs with different k values. So, it will perform better than other assemblers.
Remarque If you use our assembler in your research, please cite our papers. Peng, Y., et al. (2010) IDBA- A Practical Iterative de Bruijn Graph De Novo Assembler. RECOMB. Lisbon.
|Run Unix # idba_ud -r read.fa -o output_dir||Run Web #|
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.
|Run Unix # kmergenie ||Run Web #|
Mapsembler is a targeted assembly software. It takes as input a set of NGS raw reads and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-coherent starter, Mapsembler outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice.
Remarque Citation: Peterlongo, P., & Chikhi, R. (2012). Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer. BMC Bioinformatics, 13(1), 48. doi:10.1186/1471-2105-13-48.
|Run Unix # mapsembler ||Run Web #|
MaSuRCA is 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).
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Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet).
Remarque PDF and Citation R. Chikhi, G. Rizk. Space-efficient and exact de Bruijn graph representation based on a Bloom filter, WABI 2012
|Run Unix # minia fasta_file kmer_size min_abundance estimated_genome_size prefix||Run Web #|
De novo transcriptome assembler for very short reads
|Run Unix # oases||Run Web #|
QUality ASsesment Tool for Genome Assembly QUAST evaluates a quality of genome assemblies by computing various metrics and providing nice reports.
Remarque Citation : Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi and Glenn Tesler, QUAST: quality assessment tool for genome assemblies, Bioinformatics (2013) 29 (8): 1072-1075. doi: 10.1093/bioinformatics/btt086 First published online: February 19, 2013
|Run Unix # quast.py [options] ||Run Web #|
Ray is a parallel de novo genome assembler that utilises the message-passing interface everywhere and is implemented using peer-to-peer communication.
Remarque Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. Sébastien Boisvert, François Laviolette, and Jacques Corbeil. Journal of Computational Biology (Mary Ann Liebert, Inc. publishers). November 2010, 17(11): 1519-1533. doi:10.1089/cmb.2009.0238
|Run Unix # Ray -help||Run Web #|
SSPACE is not a de novo assembler, it is used after a preassembled run. SSPACE is a script to extend and scaffold preassembled contigs using a number of mate pairs or paired-end libraries. It uses Bowtie to map all the reads to the pre-assembled contigs. Unmapped reads are used for extending, if desired, the pre-assembled contigs with the SSAKE assembler. Again Bowtie is used to map the reads to the extended contigs. Positions and orientation of the reads are stored and used for scaffolding. If both reads of a pair are found within the allowed distance, they are used for scaffolding to determine the orientation, contig pairing and ordering of the contigs.
|Run Unix # /usr/local/genome/SSPACE-BASIC-2.0_linux-x86_64/SSPACE_Basic_v2.0.pl||Run Web #|
The Staden Package is a set of tools covering sequence assembly, editing and analysis. Gap4 performs sequence assembly, contig ordering based on read pair data, contig joining based on sequence comparisons, assembly checking, repeat searching, experiment suggestion, read pair analysis and contig editing. Pregap4 provides a graphical user interface to set up the processing required to prepare trace data for assembly or analysis. Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and ZTR trace files. Prefinish analyses partially completed sequence assemblies and suggests the most efficient set of experiments to help finish the project. Tracediff and hetscan automatically locate mutations by comparing trace data against reference traces. Spin analyses nucleotide sequences to find genes, restriction sites, motifs, etc. It can perform translations, find open reading frames, count codons, etc.
|Run Unix # http://staden.sourceforge.net/overview.html||Run Web #|
Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.
|Run Unix # tablet||Run Web #|