博文
metagenome分析中涉及到的工具
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FastQC: Quality control tool for high-throughput sequence data using modular options and giving graphic results of quality per base sequence, GC content, Nnumbers, duplication, and over represent (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Fastx-Toolkit: Command line tools for Short-reads quality control. These allow processing, cutting, format conversion, and collapsing by sequence length and identity (http://hannonlab.cshl.edu/fastx_toolkit/index.html)
PRINTSEQ: Quality control tool for sequence trimming based in dinucleotide occurrence and sequence duplication(mainly 5′/3′) (http://prinseq.sourceforge.net/)
NGS QC Toolkit: Tool for quality control analysis performed in parallel environment (http://www.nipgr.res.in/ngsqctoolkit.html)
Meta-QC-Chain: Parallel environment tool for quality control. This performs a mapping against 18S rRNA databases for removing eukaryotic contaminant sequences (http://www.computationalbioenergy.org/qc-chain.html)
Mothur: From reads quality analysis to taxonomic classification, calculus of diversity estimators and ribosomal gene metaprofiling comparison (http://www.mothur.org/)
QIIME: Quality pre-treatment of raw reads, taxonomic annotation, calculus of diversity estimators, and comparison of metaprofiling or metagenomic data (http://qiime.org/)
MEGAN: Taxonomy and functional analysis of metagenomic reads. It based on BLAST output of short reads and performs comparative metagenomics. Graphical interface (http://ab.inf.uni-tuebingen.de/software/megan5/)
CARMA: Phylogenetic classification of reads based on Pfam conserved domains (http://omictools.com/carma-s1021.html)
PICRUSt: Predictor of metabolic potential from taxonomic information obtained of 16S rRNA metaprofiling projects (http://picrust.github.io/picrust/)
Parallel-meta: Taxonomic annotation of ribosomal gene markers sequences obtained by metaprofiling or metagenomic reads. Functional annotation based on BLAST best hits results. Comparative metagenomics (
http://www.computationalbioenergy.org/parallel-meta.html)
MOCAT: Pipeline that includes quality treatment of metagenomic reads, taxonomic annotation based on single copy marker genes classification, and gene-coding prediction (http://vm-lux.embl.de/~kultima/MOCAT2/index.html)
TETRA: Taxonomic classification by comparison of tetranucleotide patterns. Web service available (http://omictools.com/tetra-s1030.html)
PhylophytiaS: Composition-based classifier of sequences based on reference genomes signatures (http://omictools.com/phylopythia-s1455.html)
MetaclusterTA: Taxonomic annotation based on binning of readsand contigs. Dependent of reference genomes (http://i.cs.hku.hk/~alse/MetaCluster/)
MaxBin: Unsupervised binning of metagenomic short reads and contigs (http://sourceforge.net/projects/maxbin/)
Amphora and Amphora2: Metagenomic phylotyping by single copy phylogenetic marker genes classification (http://pitgroup.org/amphoranet/)
BWA: Algorithm for mapping short-low-divergent sequences to large references. Based on Burrows–Wheeler transform (http://bio-bwa.sourceforge.net/)
Bowtie: Fast short read aligner to long reference sequences based on Burrows–Wheeler transform (http://bowtie-bio.sourceforge.net/index.shtml)
Genometa: Taxonomic and functional annotation of short-reads metagenomic data. Graphical interface (http://genomics1.mh-hannover.de/genometa/)
SORT-Items: Taxonomic annotation by alignment-based orthology of metagenomic reads (http://metagenomics.atc.tcs.com/binning/SOrt-ITEMS)
DiScRIBinATE: Taxonomic assignment by BLASTx best hits classification of reads (http://metagenomics.atc.tcs.com/binning/DiScRIBinATE)
IDBA-UD: Assembler de novo of metagenomic sequences with uneven depth (http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/)
MetaVelvet: De novo assembler of metagenomic short reads (http://metavelvet.dna.bio.keio.ac.jp/)
Ray Meta: Assembler of de novo of metagenomic reads and taxonomy profiler by Ray Communities (http://denovoassembler.sourceforge.net/)
MetaGeneMark: Gene coding sequences predictor from metagenomic sequences by heuristic model (http://exon.gatech.edu/index.html)
GlimmerMG: Gene coding sequences predictor from metagenomic sequences by unsupervised clustering (http://www.cbcb.umd.edu/software/glimmer-mg/)
FragGeneScan: Gene coding sequences predictor from short reads (http://sourceforge.net/projects/fraggenescan/)
CD-HIT: Clustering and comparing sequences of nucleotides or protein (http://weizhongli-lab.org/cd-hit/)
HMMER3: Hidden Markov models applied in sequences alignments (http://hmmer.janelia.org/)
BLASTX: Basic local alignment of translated sequences (http://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?PROGRAM=blastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome)
MetaORFA: Assembly of peptides obtained from predicted ORFs
MinPath: Reconstruction of pathways from protein family predictions (http://omics.informatics.indiana.edu/MinPath/)
MetaPath: Identification of metabolic pathways differentially abundant among metagenomic samples (http://metapath.cbcb.umd.edu/)
GhostKOALA: KEGG’s internal annotator of metagenomes by k-number assignment by GHOSTX searches against a non-redundant database of KEGG genes (http://www.kegg.jp/ghostkoala/)
RAMMCAP: Metagenomic functional annotation and data clustering (http://weizhong-lab.ucsd.edu/rammcap/cgi-bin/rammcap.cgi)
ProViDE: Analysis of viral diversity in metagenomic samples (http://metagenomics.atc.tcs.com/binning/ProViDE/)
Phyloseq: Tool-kit to row reads pre-processing, diversity analysis and graphics production. R, Bioconductor package (https://joey711.github.io/phyloseq/)
MetagenomeSeq: Analysis of differentially abundance of 16S rRNA gene in metaprofiling data. R, Bioconductor package (http://bioconductor.org/packages/release/bioc/html/metagenomeSeq.html)
ShotgunFunctionalizeR: Metagenomic functional comparison at level of individual genes (COG and EC numbers) and complete pathways. R, Bioconductor package (http://shotgun.math.chalmers.se/)
Galaxy portal: Web repository of computational tools that can be run without informatic expertise. Graphical interfaceand free service (https://usegalaxy.org/)
MG-RAST: Taxonomic and functional annotation, comparative metagenomics. Graphical interface, web portal, andfree service (http://metagenomics.anl.gov/)
IMG/M: Functional annotation, phylogenetic distribution of genes and comparative metagenomics. Graphical interface, web portal, and free service (https://img.jgi.doe.gov/cgi-bin/m/main.cgi)
参考文章：The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics （http://journal.frontiersin.org/article/10.3389/fgene.2015.00348/abstract）
https://blog.sciencenet.cn/blog-306699-949480.html
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