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Results for "consensus"

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• • Jit@jit.aber

  

  Understanding #Overlap Layout #Consensus #assembly http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_olc.pdf #OLC #Assembly

  Tags: Overlap, Consensus, assembly, OLC, Assembly

  2610 days ago

• • Neelam Jha@neelam

  

  Consensus of nucleotide sequences https://www.perlmonks.org/bare/?node_id=500962 #Consensus #Nucleotide #DNA

  Tags: Consensus, Nucleotide, DNA

  2024 days ago

• • Neelam Jha@neelam

  

  Generate consensus from BAM file samtools mpileup -uf chr5B_leaf_rust.fasta M27454_5B_reads_sorted.bam | bcftools call -c | vcfutils.pl vcf2fq #BAM #Consensus

  Tags: BAM, Consensus

  2024 days ago

• • Jit@jit.aber

  

  #Calculate The #Frequency Of Letters In A Biological Sequence, Or The #Consensus Matrix Of A Set Of Sequences https://www.rdocumentation.org/packages/Biostrings/versions/2.40.2/topics/letterFrequency

  Tags: Calculate, Frequency, Consensus

  1515 days ago

• • Jit@jit.aber

  

  DISCO : multi threaded and multiprocess distributed memory overlap-layout-consensus (OLC) metagenome assembler

  DISCO is a multi threaded and multiprocess distributed memory overlap-layout-consensus (OLC) metagenome assembler. Disco was developed as a scalable assembler to assemble large metagenomes from billions of Illumina sequencing reads of complex microbial communities. Disco was parallelized for...

  Tags: multiprocess, distributed, memory, overlap, layout, consensus, OLC, metagenome, assembler

  2482 days ago

• • Jit@jit.aber

  

  miniasm: very fast OLC-based de novo assembler for noisy long reads

  Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. I...

  Tags: Ultrafast, de novo, assembly, long, noisy, reads, consensus

  2342 days ago

• • Jit@jit.aber

  

  proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

  proovread : large-scale high-accuracy PacBio correction through iterative short read consensus outperforms PacBioToCA/LSC in terms of accuracy and contiguity/sensitivity (http://dx.doi.org/10.1093/bioinformatics/btu392) is easy to install/run/configure supports various types of dat HiSeq/...

  Tags: proovread, large-scale, high-accuracy, PacBio, correction, iterative, read, consensus

  2304 days ago

• • Jit@jit.aber

  

  how to polish a genome assembly https://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html #polish #nanopolish #ont #nanopore #consensus

  Tags: polish, nanopolish, ont, nanopore, consensus

  1924 days ago

• • Jit@jit.aber

  

  Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data

  Run a pipeline processing fast5s to a consensus in a single command. Recommended fixed "standard" and "fast" pipelines. Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath. Seemless distribution of tasks over local or distribute...

  Tags: Katuali, flexible, consensus, pipeline, Snakemake, basecall, assemble, polish, Oxford, Nanopore, Technology, sequencing, data

  1922 days ago

• • Abhimanyu Singh@abhimanyu

  

  Scripts to help transposable elements consensus sequences curation https://github.com/4ureliek/ReannTE #Transposable #TE #consensus #ReannTE

  Tags: Transposable, TE, consensus, ReannTE

  1787 days ago

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