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Metagenomics
Metagenomics
Wiki
Alpha and beta diversity
Contigs
Coverage depth
DNA sequencing library
Environmental gene tags (EGTs)
Fecal microbiota transplant
GC content
Giga base pairs
Horizontal gene transfer (HGT)
Lowest Common Ancestor (LCA)
Marker gene analysis
Metatranscriptomics
RNA-seq versus microarray
Microbial ecosystem
Multilocus sequence typing (MLST)
Multiplex sequencing
Operational taxonomic unit (OTU)
Orthologs and paralogs
Pangenome
Phred score (Q score)
Phylogenetics
Long branch attraction (LBA)
Ribosomal sequences 16S
16s vs shotgun
RPKM calculation
Sampling depth
Calculate sampling depth
Genome assembly
N50 statistics
Short read mapping
Soil metagenomics
Strain-level metagenomics
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
Phylogenetic tree
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
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
Fastq file format
NCBI SRA file format
Error
path not found while resolving tree within virtual file system module
Install SRA-tools
prefetch
wget download
Quality control
Trim Galore
Remove host sequences
Remove too short reads from fastq files
Ubuntu/Linux server
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
Replace string in file
rsync
Sed
shell stderr redirect
Show disk space usage
Sorting
split large file
Transpose table
word frequencies
Metagenomics
Data
Public available data - whole genome shotgun sequencing
→ NCBI
→ EMBL-EBI
→ JGI-GOLD
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