K-mer Counting for Genome with Scaffold & Contigs Assembly Level
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
implementation of k-mer counting from krakenuniq to kraken2
written by aziznasr1920 •Hello, I read that Kraken2 support now k-mer counting from KrakenUniq. Can anyone help me in the implementation of this feature on Kraken2. Thanks in …
-
Extracting k-mer counts from multiple genome sequence files
written by yas •Good day everyone, I am new here. So, I have downloaded 8 completed genome fasta files for 8 strains of *Bacillus* *subtilis* spp. My aim …
-
Variant calling for scaffold genome
written by DmissB •Hey all, I am working on a triploid non-model organism. We have only a genome at scaffold level (~37k scaffolds, 10k-25k scaffold size, and ~1.8Gbp …
-
Does Jellyfish k-mer counting tool give wrong k-mers?
written by rubyeat88 •I have just experienced a strange thing in Jellyfish. While counting k-mers using Jellyfish, some k-mers generated which is not in main DNA sequence but …
-
Annotation of contigs through Genome assembly
written by Chikitow •Hello, So I'm using a local tool to annotate several relevant k-mer contigs. It uses both Fasta and GFF from Human Genome Reference assembly 38, …
-
Genome Annotation, specific pipeline
written by bioinfo •hello everyone im facing some difficulties to re annotate mygene, i been reading a lot about and i'm kind of lost , im working with …
-
Jellyfish-Kmer, Genome Size Estimation
written by jackuser1979<p>I have filtered paired-end genomic DNA sequence of non-model plant, sequenced through Hiseq 2000.Now I want to do k-mer analysis and want to estimate genome …
-
K-Mer Counting From Single-End, Paired-End And Mate-Pair Reads
written by Alice<p>Hello, biostars!</p> <p>I had one small issue, which grew up in a big question.</p> <p>My issue is following: i'm going to count k-mers and it's …
-
Quantifying The Area Under A K-Mer Frequency Distribution Curve To Estimate Heterozygosity
written by jomaco<p>Hi,</p> <p>I have produced a k-mer frequency distribution curve using Jellyfish 1.1.11. It has a clear bi-modal distribution suggesting the sample used to produce it …
-
Tool: Jellyfish - Fast, Parallel K-Mer Counting For Dna
written by Istvan AlbertJELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of …
you are probably looking for something else than yes or no answers - jellyfish can be used on any DNA sequence, it does not care whether it is a complete or incomplete sequence
Thank you for the answer!