Results for "assembly"
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String graph based genome assembly software and tools !
In graph theory, a string graph is an intersection graph of curves in the plane; each curve is called a "string". String graphs were first proposed by E. W. Myers in a 2005 publication. In recent Genome Research paper describing an...Tags: String, graph, genome, assembly, software, tools !
2320 days ago
Converting a VCF into a FASTA given some reference !
Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does this, the function vcf2fq (lines 469-528) This script has been modified by others to convert InDels as well, e.g. this by David Eccles ./vcf2fq.pl -f <input.fasta> <all-site.vcf> ...Tags: Convert, VCF, FASTA, reference, genome, assembly, phase
2107 days ago
CANU genome assembly parameters !
Choose the appropriate parameters to run Canu and run it. The assembly will take about an hour. You can use two cores (parameter -maxThreads=2) and you would like to disable cluster option, since we compute on a single Amazon server set off the option to compute on cluster useGrid=false...Tags: CANU, genome, assembly, parameters, NGS, LongReads, OLC
1936 days ago
List of tools frequently used while genome assembly
List of tools frequently used while genome assembly: I have used the following assemblers Spades (v. 3.10.1) CANU (v. 1.6) Unicycler (v. v0.4.1) Miniasm (v. 0.2-r137-dirty) I have used the following mappers minimap2 (v. 2.0rc1-r232) minimap (v. 0.2...Tags: List, tools, frequently, genome, assembly
1921 days ago
Software for genome assembly !
List of bioinformatics tools/Software Website References for genome assembly: 1 Falcon https://github.com/PacificBiosciences/pb-assembly 2 Canu assembler http://canu.readthedocs.io/en/latest/index.html 3 Miniasm assembler https://github.com/lh3/miniasm 4 PBJelly scaffolding tool https://...Tags: List, bioinformatics, tools, Software, Website, References, genome, assembly
1335 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (cat) Read QC (FastQC) Adapter trimming (fastp) Removal of host reads (Kraken 2; optional) Variant calling Read alignment (Bowtie 2) Sort and index alignments (SAMtools) Primer sequence removal (iVar; amplicon data only) Duplicate read marking (p...Tags: assembly, pipeline, genome, illumina
869 days ago
Installing Bandage on Ubunty !
The following instructions successfully build Bandage (https://github.com/rrwick/Bandage ) on a fresh installation of Ubuntu 14.04: Ensure the package lists are up-to-date: sudo apt-get update Install prerequisite packages: sudo apt-get install build-essential git qtbase5-dev libqt5...Tags: Install, Bandage, Ubuntu, Linux, Make, Tools, Genome, Assembly
2181 days ago
- Download this https://github.com/trinityrnaseq/trinityrnaseq/releases/tag/Trinity-v2.6.6 ➜ cd trinityrnaseq-Trinity-v2.6.6 ➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ make Using gnu compiler for Inchworm and Chrysalis cd Inchworm && (test -e configure || autoreconf) \ ...
Tags: Installing, Trinity, RNA-seq, NGS, Assembly, Transcriptomics
2125 days ago
Protocol for De novo Genome Assembly using Illumina Reads
In this protocol, we address and describe the de novo assembly method for small to medium-sized genomes. What is de novo genome assembly?The method of taking a large number of short DNA sequences and placing them back together to create a reflection of the original chromosomes from which the DNA...Tags: Protocol, De novo, Genome, Assembly, Illumina, Reads
1196 days ago
