2636 days ago
ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data
ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabili...tic method that estimates the ploidy of any given contig/scaffold based on its allele...ugh sequencing coverage is available, or the true contig ploidy is low. https:/...2628 days ago
2621 days ago
2558 days ago
CLA: Contig-Layout-Authenticator
...h Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, resul...e ordering and scaffolding of large repetitive contigs. The tool has been validated...2558 days ago
2542 days ago
GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
...uencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which combines contig order, distance and orientati...2540 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...sets and 3 out of 4 ONT datasets into a single contig. The 12 PacBio data sets are&...erial genomes, it is possible to generate long contigs from raw PacBio or ONT reads...old > reads.fa And then count how many contigs: grep ">" reads.fa | w...2352 days ago
Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
...erform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: the contig N50 length is more than ten-t...2350 days ago
Genome assembly stats plotting
...novo genome assembly can be summarised b y a number of metrics, including: Overall assembly length Number of scaffolds/contigs Length of longest scaffold/contig Scaffold/contig N50 and N90A...2259 days ago