Results for "genome"
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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
2104 days ago
Nanopolis: polish a genome assembly
Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below). Quickst...Tags: Nanopolis, polish, ONT, nanopore, genome, assembly, ngs
2099 days ago
My commonly used commands in Bioinformatics
FYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually: minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta racon_assembly.fasta nucmer -p nucmer assembly.fasta racon_assembly....Tags: my, commands, ngs, genome
2099 days ago
GFinisher: a new strategy to refine and finish bacterial genome assemblies
GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references. java -Xms2G -Xmx4G -jar GenomeFinisher.jar \ -i target_contigs.fasta \ ...Tags: GFinisher, strategy, refine, finish, bacterial, genome, assemblies
2098 days ago
LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds using BWA mem algorithm in BWA package. In the pa...Tags: LR_Gapcloser, tiling, path-based, gap, closer, long, reads, complete, genome, assembly
1440 days ago
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides another practical alternative to existing mate-...Tags: P_RNA_scaffolder, fast, accurate, genome, scaffolder, paired-end, RNA, sequencing, reads, scaffold
2056 days ago
- HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (≥3%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a hierarchical scaffolding procedure and a reliabl...
Tags: HaploMerger2, rebuild, haploid, sub-assemblies, high-heterozygosity, diploid, genome, assembly
2035 days ago
- GRSR is a Tool for Deriving Genome Rearrangement Scenarios for Multiple Uni-chromosomal Genomes. This tool will do the following steps: Step 1. Run mugsy to get multiple sequence alignment results. Step 2 & 3. Extraction of the Coordinates of Core Blocks, Construction of Synteny Blocks an...
Tags: GRSR, tool, genome, rearrangement, scenarios, multiple, unichromosomal, genome, sequences
2034 days ago
- This is a tutorial for a workshop on long-read (PacBio) genome assembly. It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and correcting the assembly with short-read Illumina data....
Tags: longread, ngs, assembly, genome, reads, tutorial
2028 days ago
