Whar are N50 and L50 of a contig assembly file? How to calculate it?
I am currently dealing with new contig assembly dataset, and bit confused about N50 and L50 stuff ....Tags: NGS, N50, L50, Contig, Assembly, Genome
2976 days ago
Tags: Blastn, BLAST, Nucleotide, Alignment, Database, NR, Contig, NGS
2868 days ago
Tags: Bioinformatics, SSPACE, Scaffolding, NGS, Genome, Contig
2549 days ago
CLA: Contig-Layout-Authenticator
To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, resulting in better assembled genomes. Moreover, CL...Tags: Bioinformatics, Analysis, Scaffolding, CLA, Contig
2549 days ago
PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of existing contigs. Initially, thos...Tags: PRICE, Paired-Read, Iterative, Contig, Extension, de novo, genome, assembler, C++.
2147 days ago
MEC: Contig Misassembly Correction
MEC, to identify and correct misassemblies in contigs. Firstly, MEC takes fragment coverage as the feature to detect the candidate misassemblies. Then, it can distinguish a large number of false positives from the candidate misassemblies based on the distribution of paired-end reads and the stati...Tags: MEC, Contig, Misassembly, Correction, assembly
1543 days ago
Multi-CAR: a tool of contig scaffolding using multiple references
we design a simple heuristic method to further revise our single reference-based scaffolding tool CAR into a new one called Multi-CAR such that it can utilize multiple complete genomes of related organisms as references to more accurately order and orient the contigs of a draft genome. In practic...Tags: Multi-CAR, tool, contig, scaffolding, multiple, references
2244 days ago
Tags: GMcloser, close, gaps, assemblies, accurately, likelihood-based, selection, contig, long-read, alignments, Genome, Assembly
2147 days ago
CSAR-web: a web server of contig scaffolding using algebraic rearrangements
CSAR-web is a web-based tool that allows the users to efficiently and accurately scaffold (i.e. order and orient) the contigs of a target draft genome based on a complete or incomplete reference genome from a related organism. CSAR-web can serve as a convenient and useful scaffolding tool ...Tags: CSAR-web, web, server, contig, scaffolding, algebraic, rearrangements
1478 days ago