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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
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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
Tree-construction
Phylogenetic tree
Phylogenetic tree construction tools
→ RAxML
→ FastTree
→ IQ-TREE
see also
→ Wikipedia - List of phylogenetics software
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