Results for "Reads"

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  • Metagenomics

    Metagenomics

    Metagenomics is the study of genetic material from environmental samples to characterize and identify the millions of microbes from these samples. Example: Gut microbiome, soil sample, water, etc. More information: http://www.nature.com/nrmicro/focus/metagenomics/index.html http://www.ploscom...

    Tags: metagenomics, metatranscriptomics, genomics, reads, 16S rRNA, microbes, microbiology, ecogenomics, ecology, microbiome

    1172 days ago

  • #Mapping #sequencing #reads to a #reference #genome with #Bowtie2: a step-by-step guide https://insidedna.me/tutorials/view/how-to-use-bowtie2-read-mapping

    Tags: Mapping, sequencing, reads, reference, genome, Bowtie2

    443 days ago

  • Assemble short reads http://ged.msu.edu/angus/tutorials/short-read-assembly.html #Tutorial #ABySS #Bacteria #Reads #Assembly #Genomics #NGS

    Tags: Tutorial, ABySS, Bacteria, Reads, Assembly, Genomics, NGS

    1089 days ago

  • Reference-free Prediction of Rearrangement Breakpoint Reads http://bioinformatics.oxfordjournals.org/content/early/2014/05/28/bioinformatics.btu360.short #Reference #Breakpoint #Reads #Rearrangement

    Tags: Reference, Breakpoint, Reads, Rearrangement

    988 days ago

  • Stacks

    Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeogr...

    Tags: Bioinformatics, Computational Biology, Reads, RAD-Seq, NGS

    461 days ago

  • RACA: Reference-Assisted Chromosome Assembly

    Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads. http://www.ncbi.nlm.nih.gov/pubmed/23307812 http://bioen-comp...

    Tags: Bioinformatics, NGS, Assembly, Reference, RACA, Reads

    419 days ago

  • Trimmomatic: A flexible read trimming tool for Illumina NGS data

    Paired End: java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 ...

    Tags: Bioinformatics, Trim, NGS, Illumina, Reads, Trimmomatic

    410 days ago

  • SPAdes

    SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8, 2016 and can be downloaded from http://bioinf.spbau...

    Tags: Bioinformatics, NGS, Assembly, Assembler, SPAdes, Reads, Illumina

    406 days ago

  • ALE: a Generic Assembly Likelihood Evaluation Framework for Assessing the Accuracy of Genome and Metagenome Assemblies

    Assembly Likelihood Evaluation (ALE) framework that overcomes these limitations, systematically evaluating the accuracy of an assembly in a reference-independent manner using rigorous statistical methods. This framework is comprehensive, and integrates read quality, mate pair orientation and inse...

    Tags: Bioinformatics, FASTQ, NGS, ALE, Framework, Stats, Reads, Evaluation, Quality, Assembly

    399 days ago

  • mrFAST: Micro Read Fast Alignment Search Tool

    mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 4+4 bp. This manual, describes ...

    Tags: Bioinformatics, FASTQ, Reads, NGS, Mapping, Alignment, Reference

    399 days ago