Protocol for De novo Genome Assembly using Illumina Reads
...rvice - http://www.jcvi.org/cms/research/projects/annotation-service/ Frequent command use for the analysis...re at: https://bioinformaticsonline.com/blog/view/38765/list-of-tools-frequently-used-while-genome-assemblyh...1215 days ago
alienness : Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life
...transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularl...2256 days ago
3571 days ago
Frequent words problem solution by Perl
Solved with perl http://rosalind.info/problems/1a/ #Find the most frequent k-mers in a string.#Given: A DNA string Text and an integer k.#Return: All most frequent k-mers in Text (in any order)...3263 days ago
Awesome perl frameworks, libraries and software - PART 3
...tovani/SPPM-Web - São Paulo Perl Mongers website. jzawodn/perl-Algorithm-TopPercent - A perl module for tracking the top-N most frequent items in a streaming data set...2504 days ago
Genome Assembly Tools and Software - PART1 !!
...tructing repeats directly from sequence reads. It based on the idea of frequent k-mer assembly. REPdenovo pro...ionalities.1.Assembly. This step performs k-mer counting. Then we find frequent k-mers whose frequencies are...2696 days ago
Frequent Paired-end reads (PE 2x100) mapping command lines
bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ &&...2192 days ago
Frequent Paired-end reads (PE 2x100) mapping command lines
bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ && bwa sampe hs37m r1.sai r2.sai r1.fq r2.fq > r12.bwa.sam bwa bwasw ../index/bwa/hs37m.fa r12.fq > r12.bwasw.sam ...Tags: Frequent, Paired-end, reads, (PE 2x100), mapping, command, lines
2192 days ago
Frequent parameters for bioinformatics tools !
Third party executable parameters and options. Trimmomatic “ILLUMINACLIP:...:2:30:10” “LEADING:15” “TRAILING:15” “SLIDINGWINDOW:4:20” “MINLEN:20” “TOPHRED33” Filtlong --min_length 500 --min...Tags: Frequent, parameters, bioinformatics, tools
1296 days ago
2147 days ago
Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
...indow to select a minimizer from. If equal to 1, minimizers will be turned off. [5] --freq-percentile FLT Filer the (1.0 - value) percent of most frequent seeds in the lookup process....2302 days ago