Metagenomics
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Metagenomics
Wiki
Tools
16S tools
Assembly
BLAST
Bowtie2
Genome
Pathogen screening
Phylogenetic tree
SAMtools
Sequence data
Short read samples
Ubuntu/Linux server
Tools
>
Short read samples
>
Quality control
Quality control & raw data processing tools
FastqMcf (
ea-utils
)
https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqMcf.md
FastQC
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
FASTX-Toolkit
http://hannonlab.cshl.edu/fastx_toolkit/
Usearch
http://www.drive5.com/usearch/manual/cmd_fastq_filter.html
Trimmomatic
http://www.usadellab.org/cms/?page=trimmomatic
Sickle
https://github.com/ucdavis-bioinformatics/sickle