Contig or scaffold N50 is a weighted median statistic such that 50% of the entire assembly is contained in contigs or scaffolds equal to or larger than this value. Mathematically: Given a set of sequences of varying lengths, the N50 length is defined as the length N for which 50% of all bases in the sequences are in a sequence of length L < N.

2021年7月3日 · Contig NG50 is defined as the length at which half of the predicted genome size is contained in contigs longer than this length. I can’t understand this and googling returned papers of similar complexity e.g.: NG50 refers to the length of the smallest contig added to cover 50% of all nt estimated in the genome; (25)...

2015年5月19日 · Can someone explain the differences between sequence, reads, and contigs of genetic material such as DNA, if possible with an example?

2017年6月1日 · I have never heard the term “contig based alignment”, and your question is the only Google hit of this exact query (apart from a 2012 patent application). That said, and without knowing the exact context, I am assuming that you are essentially right: contig-based alignment probably refers to the de novo assembly of reads into contigs, which ...

In whole-genome assembly, the BAC fragments (red line segments) and the reads from five individuals (black line segments) are combined to produce a contig and a consensus sequence (green line). The contigs are connected into scaffolds, shown in red, by pairing end sequences, which are also called mates.

2015年11月9日 · Fig1: Screen capture from DNA Baser Assembler of an 'assembly to reference'. The reference is in purple color. The forward and reverse sequences are red and green. The contig is blue. Note about the input of the two processes: The sequences that enter into an alignment have (supposedly) already been cleaned up. Every base is correct/accurate.

2015年7月6日 · Classically, the linkage between two loci can be measured in centimorgans (cM), which represents the percent chance that these two loci will recombine an odd number of times (generating a recombinant

As a consequence, you instead end up with distinct, contiguous blocks (“contigs”) of mapped reads. Each contig is a sequence fragment, like reads, but much larger (and hopefully with less errors). Assembly. Sometimes you want to sequence a new organism so you don’t have a reference sequence to map to. Instead, you need to do a de novo ...

2021年3月6日 · The first gap in the ordered short-read assembly (left-most red line in the figure) occurs at position 15,085 in the first contig and is 320 bp long. Looking at the same region in the long-read assembly, this closely corresponds to a 236 bp tandem repeat (CTGG × 59) at position 14,848. The authors of the short-read paper used 150 bp paired-end ...

2017年5月12日 · Stack Exchange Network. Stack Exchange network consists of 183 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers.