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Results for "bam"

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• • Neelam Jha@neelam

  

  Comment on "REAPR: a universal tool for genome assembly evaluation"

  ...nute. The next tool we need is reapr smaltmap which creates a bam file of read-pair mappings. D...ctmap and create an output file called <assembler>_smalt.bam. This should take about twent...

  1327 days ago

• • Jit@jit.aber

  

  Comment on "ASCIIGenome: genome browser based on command line interface and designed for running from console terminals."

  ...nbsp;      Set display to reads per million for BAM and TDF files.  &nb...p;          setGenome fasta|bam|genome    ...

  1510 days ago

• • Rahul Nayak@rahul

  

  Comment on "Nanopolis: polish a genome assembly"

  ...ont2d -t 8 draft.fa reads.fa | samtools sort -o reads.sorted.bam -T reads.tmp - samtools index reads.sorted.bam python nanopolish_makerange....ensus -o polished.{1}.vcf -w {1} -r reads.fa -b reads.sorted.bam -g draft.fa -t 4 --min-candid...

  2089 days ago

• • Jit@jit.aber

  

  Comment on "AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data"

  ...developed in Java. Import of data is possible from FastQfiles, BAM or SAM format. This tool prov...the GenePattern web interface. The input could be one or more BAM files. HTML reports are gener...

  2127 days ago

• • Jit@jit.aber

  

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

  ...D-tag based). (software?) BioNanoGenomics can be used for QC also Use a genome browser to get a feeling for your results, e.g. IGV; add assembly, BAM files, annotation, transcript...

  2921 days ago

• • Jitendra Narayan@admin

  

  Comment on "Alignment of closely related whole genomes/scaffolds"

  ...o used BWA-SW, BLAT and LASTZ. However, LASTZ is not well-suited for aligning to many chromosomes at once. Whereas, the BLAT is difficult as PSL to BAM conversion is imperfect in it...

  3009 days ago