Results for "haploid"
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CovCal: Coverage / Read Count Calculator
...milar calculator written by James Hadfield. Coverage is calculated as C=LN/G and reads as N=CG/L where C = Coverage (X),L = Read length (bp), G = Haploid genome size (bp), and N = Num...2178 days ago
- ...horter than around 80nt, or reads where the base qualities are low in all or most reads before 60nt. A5-miseq assumes it is assembling homozygous haploid genomes. Use a different asse...
2829 days ago
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Top-level pages
List of Bioinformatics Software Tools for Next Generation Sequencing
...at has been aligned in BWA and Samtools Output: BCF that can be formatted to VCF using bcftools Snippy Description: finds indels between haploid reference genome and NGS sequ...2921 days ago
Genome Assembly Tools and Software - PART1 !!
...eep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia stipitis. C...2698 days ago
Wire posts
Bio-Scripts
- ...h=100000 \ out=/dev/null # make 60x haploid coverage for Illumina reads...d+"` echo "best k=${k}" # make 30x haploid coverage for PacBio CLR reads...andom_reads_pacbio.log 2>&1 # make 30x haploid coverage for PacBio reads for...
940 days ago
Bash script to simulate a genome !
...midlength=20000 maxlength=100000 \ out=/dev/null # make 60x haploid coverage for Illumina reads...w-reads.log | grep -Po "\d+"` echo "best k=${k}" # make 30x haploid coverage for PacBio CLR reads...930 days ago
Tags
Snippy: Rapid haploid variant calling and core SNP phylogeny
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produces a cons...Tags: Snippy, Rapid, haploid, variant, calling, core, SNP, phylogeny, bacteria
2037 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
2059 days ago
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Comments
- ...tory is created if needed. It is not possible to run multiple assemblies in the same directory. The genome size should be your best guess of the haploid genome size of what is being...
2111 days ago
