Metagenomics
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Metagenomics
Wiki
Tools
16S tools
Assembly
BLAST
Bowtie2
Genome
Pathogen screening
Phylogenetic tree
SAMtools
Sequence data
Shotgun sequencing
Ubuntu/Linux server
Tools
>
Shotgun sequencing
Short read samples from full genome shotgun sequencing
→ Alignment tools
Bowtie2, BWA,...
→ Assembly tools
SPAdes, MEGAHIT,...
→ Pathogen screening
screen for marker genes or strains in short-read samples
Subpages
(7):
Alignment
Data
Fastq file format
NCBI SRA file format
Quality control
Remove host sequences
Remove too short reads from fastq files