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Title
SAMSA2: a standalone metatranscriptome analysis pipeline
Authors
Keywords
Metatranscriptomics, Metagenomics, Pipeline, Software, Bioinformatics, Open access, Annotation, Functions, Metatranscriptome, RNA-seq, Cluster, GALAXY, Tool, Microbiome, Bacteria, SAMSA
Journal
BMC BIOINFORMATICS
Volume 19, Issue 1, Pages -
Publisher
Springer Nature
Online
2018-05-21
DOI
10.1186/s12859-018-2189-z
References
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Related references
Note: Only part of the references are listed.- SAMSA: a comprehensive metatranscriptome analysis pipeline
- (2016) Samuel T. Westreich et al. BMC BIOINFORMATICS
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- (2016) Mark Davids et al. PLoS One
- MetaTrans: an open-source pipeline for metatranscriptomics
- (2016) Xavier Martinez et al. Scientific Reports
- Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis
- (2015) Yuzhen Ye et al. BIOINFORMATICS
- IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information
- (2015) Henry C.M. Leung et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Anvi’o: an advanced analysis and visualization platform for ‘omics data
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- Fast and sensitive protein alignment using DIAMOND
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- Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation
- (2014) Albi Celaj et al. Microbiome
- PEAR: a fast and accurate Illumina Paired-End reAd mergeR
- (2013) J. Zhang et al. BIOINFORMATICS
- A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets
- (2013) Milkha M Leimena et al. BMC GENOMICS
- IDBA-MT: De Novo Assembler for Metatranscriptomic Data Generated from Next-Generation Sequencing Technology
- (2013) Henry C.M. Leung et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
- (2013) Ross Overbeek et al. NUCLEIC ACIDS RESEARCH
- RefSeq microbial genomes database: new representation and annotation strategy
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- Data, information, knowledge and principle: back to metabolism in KEGG
- (2013) Minoru Kanehisa et al. NUCLEIC ACIDS RESEARCH
- SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
- (2012) Evguenia Kopylova et al. BIOINFORMATICS
- An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
- (2011) Daniel McDonald et al. ISME Journal
- The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
- (2008) F Meyer et al. BMC BIOINFORMATICS
- The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
- (2008) B. L. Cantarel et al. NUCLEIC ACIDS RESEARCH
- MetaSim—A Sequencing Simulator for Genomics and Metagenomics
- (2008) Daniel C. Richter et al. PLoS One
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