Software and supporting data for "Fast-SG: An alignment-free algorithm for hybrid assembly"
Dataset type: Genomic, Software
Data released on April 24, 2018
Di Genova A; Ruz GA; Sagot MF; Maass A (2018): Software and supporting data for "Fast-SG: An alignment-free algorithm for hybrid assembly" GigaScience Database. http://dx.doi.org/10.5524/100437
Long read sequencing technologies are the ultimate solution for genome repeats, allowing near reference level reconstructions of large genomes. However, long read de novo assembly pipelines are computationally intense and require a considerable amount of coverage, thereby hindering their broad application to the assembly of large genomes. Alternatively, hybrid assembly methods which combine short and long read sequencing technologies can reduce the time and cost required to produce de novo assemblies of large genomes. Here, we propose a new method, called Fast-SG, which uses a new ultra-fast alignment-free algorithm specifically designed for constructing a scaffolding graph using light-weight data structures.Fast-SG can construct the graph from either short or long reads. This allows the reuse of efficient algorithms designed for short read data and permits the definition of novel modular hybrid assembly pipelines. Using comprehensive standard datasets and benchmarks, we show how Fast-SG outperforms the state-of-the-art short read aligners when building the scaffolding graph, and can be used to extract linking information from either raw or error-corrected long reads. We also show how a hybrid assembly approach using Fast-SG with shallow long read coverage (5X) and moderate computational resources can produce long-range and accurate reconstructions of the genomes of Arabidopsis thaliana (Ler-0) and human (NA12878).
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(PubMed: 29741627)
Additional information:
Sample ID | Taxonomic ID | Common Name | Genbank Name | Scientific Name | Sample Attributes |
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A. thaliana (Ler-0) | 3702 | mouse-ear cress | thale cress | Arabidopsis thaliana | Description:Representative sample of Arabidopsis thaliana sequences used for demonstration of sequence assembly tools Sequencing method:Illumina, PacBio Relevant electronic resources:http://labshare.cshl.edu/shares/schatzlab/www-data/ectools/arabidopsis/Illumina_2x300_R1.fastq.gz, http://labshare.cshl.edu/shares/schatzlab/www-data/ectools/arabidopsis/Illumina_2x300_R2.fastq.gz, https://downloads.pacbcloud.com/public/SequelData/ArabidopsisDemoData/SequenceData/1_A01_custome r/m54113_160913_184949.subreads.bam, http://gembox.cbcb.umd.edu/shared/canu/asm/canu/ |
E.coli K-12 | 83333 | Escherichia coli K-12 | Description:Representative sample of Escherichia coli K-12 sequences used for demonstration of sequence assembly tools Sequencing method:Illumina, PacBio, ONT Relevant electronic resources:http://labshare.cshl.edu/shares/schatzlab/www-data/nanocorr/2015.07.07/Ecoli_S1_L001_R1_001.fastq.gz, https://s3.amazonaws.com/files.pacb.com/datasets/secondary-analysis/e-coli-k12-8plex/Ecoli_8plex_demo.barcoded.subreads.bam, https://s3.climb.ac.uk/nanopore/E_coli_K12_1D_R9.2_SpotON_2.pass.fasta , http://labshare.cshl.edu/shares/schatzlab/www-data/ectools/ecoli/ecoli_illumina.fa.gz | ||
Human Chromosome 14 | 9606 | Human | human | Homo sapiens | Description:Representative sample of Homo sapiens ... Alternative accession-SRA File:ERR163027 Sequencing method:Illumina ... + |
NA12878 | 9606 | Human | human | Homo sapiens | Description:Representative sample of Homo sapiens sequences used for demonstration of sequence assembly tools Sequencing method:ONT Relevant electronic resources:https://github.com/nanopore-wgs-consortium/NA12878/blob/master/Genome.md, ftp://ftp.broadinstitute.org/pub/crd/Discovar/assemblies/51400.newchem/a.lines.fasta |
P_falciparum | 36329 | Plasmodium falciparum 3D7 | Description:Representative sample of Plasmodium fa... Alternative accession-SRA File:ERR034295, ERR16302... Sequencing method:Illumina ... + | ||
R_sphaeroides | 1063 | Rhodobacter sphaeroides | Description:Representative sample of Rhodobacter s... Alternative accession-SRA File:SRR034528 Sequencing method:Illumina ... + | ||
S_aureus | 1280 | Staphylococcus aureus | Description:Representative sample of Staphylococcu... Alternative accession-SRA File:SRR022865 Sequencing method:Illumina ... + | ||
S. cerevisiae W303 | 580240 | Saccharomyces cerevisiae W303 | Description:Representative sample of Saccharomyces cerevisiae W303 sequences used for demonstration of sequence assembly tools Sequencing method:PacBio Relevant electronic resources:http://labshare.cshl.edu/shares/schatzlab/www-data/ectools/w303/Pacbio.fasta.gz, http://labshare.cshl.edu/shares/schatzlab/www-data/ectools/w303/w303_illumina.fa.gz |