What is the difference between sequence, reads, and contigs of …
May 19, 2015 · My understanding of those three words as follows: sequence is a generic name describing order of biological letters (DNA/RNA or amino acids). Both contigs and reads are …
dna sequencing - What is the difference between contig- and read …
Jun 1, 2017 · Is contig based alignment refer to de novo assembly and then it is align to a reference genome. I am confused that if you have read based alignment then what is the …
Understanding Contig NG50 - Biology Stack Exchange
Jul 3, 2021 · 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 …
dna sequencing - What is the difference between sequence …
Nov 9, 2015 · 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 …
An example for N50? Why do we need it? - Biology Stack Exchange
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 …
How to identify an unknown species from its genome sequence
Oct 6, 2020 · The contig length is about 360 000 bases long. I let the query run for 30 minutes before stopping, nothing came of it. I am assuming 360 kbp is too long. I was thinking of …
What is "contigs" in Picard's ReorderSAM? - Biology Stack Exchange
ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs Q: What does contig ordering …
How exactly are gaps defined in genomics? - Biology Stack Exchange
Apr 10, 2016 · The word ‘gap’ can be used both loosely and in specific genomic contexts, as listed by @Student T. The usage that seems to relate to your question — Sequence Coverage …
What does the "cov" mean in a velvet assembler generated contig …
Jul 1, 2015 · It means k-mer coverage. From the velvet manual: 4.2.1 The contigs.fa file This fasta file contains the sequences of the contigs longer than 2 k , where k is the word-length used in …
genetics - What are primary reasons for the failure to …
Such regions will also tend to be "collapsed", meaning that you only have one contig representing a repeat that should actually be present as several contigs with different locations in the …