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Results for "contamination"

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• • Jit@jit.aber

  

  MetaBAT: An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities

  MetaBAT, An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms ...

  Tags: Bioinformatics, Analysis, Assembly, Genome, MetaBAT, MetaGenomics, Contamination

  2601 days ago

• • Jit@jit.aber

  

  COCACOLA (binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge)

  COCACOLA is a general framework that combines different types of information: sequence COmposition, CoverAge across multiple samples, CO-alignment to reference genomes and paired-end reads LinkAge to automatically bin contigs into OTUs. Furthermore, COCACOLA seamlessly embraces customized prior k...

  Tags: Bioinformatics, Analysis, Assembly, Genome, COCACOLA, MetaGenomics, Contamination

  2600 days ago

• • Jit@jit.aber

  

  Understanding Alien Index (AI) https://github.com/josephryan/alien_index #Alien @ Index #AlienIndex #AI #Contamination #Tool

  Tags: Alien, AlienIndex, AI, Contamination, Tool

  2573 days ago

• • Jit@jit.aber

  

  Decontamination https://img.jgi.doe.gov/er/doc/SingleCellDataDecontamination.pdf #Bacteria #Contamination

  Tags: Bacteria, Contamination

  2540 days ago

• • Surabhi Chaudhary@surabhi

  

  BBTools for bioinformatician !

  BBMap.sh Mapping Nanopore reads BBMap.sh has a length cap of 6kbp. Reads longer than this will be broken into 6kbp pieces and mapped independently. Code: $ mapPacBio.sh -Xmx20g k=7 in=reads.fastq ref=reference.fa maxlen=1000 minlen=200 idtag ow int=f qin=33 out=mapped1.sam minratio=0.15...

  Tags: BBMap, Map, NGS, Reads, Sam, Bam, Contamination, Filtration

  2254 days ago

• • Poonam Mahapatra@poonam

  

  TACOA: Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

  TACOA is a software that can accurately predict the taxonomic origin of genomic fragments from metagenomic data sets by combining the advantages of the k -NN approach with a smoothing kernel function. TACOA can be easily installed and run on a desktop computer, therefore allowing researchers ...

  Tags: TACOA, Taxonomic, classification, environmental, genomic, fragments, KNN, Contamination

  2166 days ago

• • BioJoker@biojoker

  

  http://www-labgtp.na.icar.cnr.it/decontaminer/ decontaMiner, a tool for detecting contaminating organisms in human unmapped sequences. #Tools #decontaMiner #Tool #Contamination

  Tags: Tools, decontaMiner, Tool, Contamination

  1816 days ago

• • Jit@jit.aber

  

  Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence

  Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in ...

  Tags: Taxoblast, pipeline, identify, contamination, genomic, sequence

  2339 days ago