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  • Genome assembly using PacBio data - Galaxy Training Network
    The Flye assembly: 13 contigs, N50 = 4 9Mb, length max = 6 8Mb, size = 38 7 Mb, 49 31% GC Genome assembly assessment with BUSCO BUSCO (Benchmarking Universal Single-Copy Orthologs) allows a measure for quantitative assessment of genome assembly based on evolutionarily informed expectations of gene content
  • Large genome assembly and polishing - Galaxy Training Network
    The assembled contigs are in the “Flye assembly on data X (consensus)” (X is a number that will vary depending on where it sits in your history) Open the Quast tabular report to see the assembly statistics: There are 153 contigs, largest is ~246,000 bp, and total length almost 10 million bp
  • Chloroplast genome assembly - Galaxy Training Network
    Assemble: Use Flye to assemble the nanopore reads, then get Fasta statistics Note: this may take several hours Polish assembly: Use Pilon to polish the assembly with short Illumina reads Note: Don’t forget to map these Illumina reads to the assembly first using bwa-mem, then use the resulting bam file as input to Pilon
  • Genome Assembly Quality Control - Galaxy Training Network
    The Flye assembly, with a genome fraction of 99 57% while Hifiasm have a low genome fraction (75 15%) which can indicate a problematic assembly The longest contig is 1,438,238 bp for Flye assembly while is 1,795,653 bp for Hifiasm; The N50 of the Flye assembly is 929,061 bp
  • Assembly Large genome assembly and polishing Assembly with Flye . . .
    DNA sequence data has become an indispensable tool for Molecular Biology Evolutionary Biology Study in these fields now require a genome sequence to work from We call this a 'Reference Sequence ' We need to build a reference for each species We do this by Genome Assembly De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone
  • Genome Assembly of MRSA from Oxford Nanopore MinION data (and . . .
    DNA sequence data has become an indispensable tool for Molecular Biology Evolutionary Biology Study in these fields now require a genome sequence to work from We call this a 'Reference Sequence ' We need to build a reference for each species We do this by Genome Assembly De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone
  • Flye: de novo assembler for single molecule sequencing reads
    Collection of tutorials developed and maintained by the worldwide Galaxy community
  • Genome Assembly using PacBio data - training. galaxyproject. org
    DNA sequence data has become an indispensable tool for Molecular Biology Evolutionary Biology Study in these fields now require a genome sequence to work from We call this a 'Reference Sequence ' We need to build a reference for each species We do this by Genome Assembly De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone
  • FAQs Chloroplast genome assembly Assembly - Galaxy Training Network
    This may happen even if running the same data with the same version of Flye It can also happen with a different version of Flye To make things more complicated (stop reading now if you would like!)… the chloroplast genome has a structure that includes repeats (the inverted repeats), and, the small-single-copy region of the chloroplast
  • FAQs Genome assembly using PacBio data Assembly
    DNA sequence data has become an indispensable tool for Molecular Biology Evolutionary Biology Study in these fields now require a genome sequence to work from We call this a 'Reference Sequence ' We need to build a reference for each species We do this by Genome Assembly De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone





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