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Metagenomics
  • Metagenomics
    • Taxonomy
      • Alpha and beta diversity
      • Strain level
      • Pangenome
      • Marker genes
        • MLST
      • 16S
        • Operational taxonomic unit (OTU)
        • 16s vs shotgun
    • Phylogeny
      • Horizontal gene transfer (HGT)
      • Lowest Common Ancestor (LCA)
      • Long branch attraction (LBA)
    • Evolution
    • Ecosystem
      • Environmental gene tags (EGTs)
      • Soil metagenomics
    • Metatranscriptomics
      • RNA-seq versus microarray
    • QC
      • Coverage depth
      • Sampling depth
        • Calculate sampling depth
      • RPKM calculation
      • Phred score (Q score)
      • Giga base pairs
      • GC content
    • Wiki
      • Microbiome
      • Orthologs and paralogs
      • Short read mapping
      • Fecal microbiota transplant
      • DNA sequencing library
      • Multiplex sequencing
      • x
      • x
      • x
      • x
        • x
      • x
      • x
      • x
  • Tools
    • 16S tools
      • DADA2
        • Conda environment
          • Segmentation fault
      • Normalization
        • CSS
      • QIIME
        • Alpha & Beta diversity
        • Install QIIME 1
          • AttributeError:axisbg
          • biom error
          • Greengenes
          • h5py BIOM error
          • PackagesNotFoundError
          • qiime_config
          • R for QIIME
          • usearch61
        • OTU biom table
          • QIIME: split OTU table
          • ValueError column index exceeds matrix dimensions
        • QIIME mapfile
        • QIIME OTU clustering
          • Error running usearch61
          • Fungi 18S
          • IOError Errno 28 No space left on device
          • SILVA
        • QIIME pre-processing
          • Cannot find fastq-join
          • join-error
          • split-error
        • Taxonomy
        • Test statistics
    • Assembly
      • Contigs
      • N50 statistics
      • MEGAHIT
    • BLAST
      • BLAST error: Too many positional arguments
      • BLAST word-size
      • BLASTn output format 6
      • BLASTx
      • E-value & Bit-score
      • FastANI
        • Install FastANI
          • Install autoconf
          • Install GLS
      • Generate_database
        • Public sequences
      • Install BLAST
      • megablast
    • Bowtie2
      • Create bowtie2 index
      • Install bowtie2
        • libtbb.so.2
        • Segmentation fault
    • Genome
      • Prokka
    • Pathogen screening
    • Phylogenetic tree
      • File format
      • Sequence-Alignment
        • Alignment viewer
      • Tree-construction
        • FastTree
        • RAxML
          • Add bipartition
          • Install RAxML
      • Tree-viewer
        • Forester
          • Java error
    • SAMtools
      • BCFtools
      • Consensus sequence
      • Converting BAM to fastq
      • Error
        • Could not parse the header line
        • different line length in sequence
      • Install
        • Error curses.h
      • Number of reads in bam file
      • SAM file format
      • SAMtools: get breadth of coverage
    • Sequence data
      • Convert fastq to fasta
      • Extract sequence subset
      • Get random subset
      • Multi-FASTA format
      • NCBI ftp genome download
        • gff to ffn
    • Shotgun sequencing
      • Alignment
        • Viewer
          • Tablet
      • Data
      • NCBI SRA files
        • Install SRA-tools
        • prefetch
        • Error
          • path not found while resolving tree within virtual file system module
        • wget download
        • old fastq-dump
      • Quality control
        • Trim Galore
      • Remove host sequences
      • Remove too short reads from fastq files
      • Fastq file format
    • Ubuntu Linux
      • awk
      • bzip2
      • Extract columns from file
      • File properties
      • gzip & tar.gz
      • Loop over list of files
        • find
        • if greater than
        • String split
      • Rename multiple files
      • rsync
      • sed
      • Shell stderr redirect
      • Show disk space usage
      • Split large file
      • Data tables
        • Transpose table
        • Sorting
    • HPC SGE cluster
      • Submit job
      • Check cluster nodes
Metagenomics

Metagenomics

Computational Tools

Exploring microbial communities in the human gut, on plant roots, or in soil and water samples.

→ Metagenomics and the microbiome



→ Metagenomics Tools

Sequence data analysis

→ BLAST → Bowtie2 → SAMtools → Assembly → Shotgun sequencing → 16S tools → Ubuntu / Linux server



→ Taxonomy (profiling)

→ Strain-level resolution → 16S OTUs

→ Phylogeny & Evolution

→ Phylogenetic trees → Horizontal gene transfer

→ Microbial ecosystem

Resistance & Resilience

→ Quality control

Coverage, quality measures, normalization


www.metagenomics.wiki

Author: Matthias Scholz

X/Twitter:  @panphlan

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