Shotgun metagenomic sequencing data analysis bioinformatics software tools

Metagenomic sequencing analysis steps

Metagenomic sequencing analysis workflow

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Metagenomic sequencing analysis workflow schema
Metagenomics is defined as the study of the metagenome, which is total genomic DNA from environmental samples. Metagenomics has long been one of the major research tools in microbial ecology since the term was first used in 1998 (Handelsman et al.,…

Shotgun metagenomic sequencing data analysis bioinformatics software tools

Most Recent Tools

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sixpack
Desktop

sixpack

Displays a DNA sequence with 6-frame translation and open reading frames…

Displays a DNA sequence with 6-frame translation and open reading frames (ORFs). sixpack reads a DNA sequence and writes an output file giving out the forward and reverse sense sequences with the…

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vectorstrip
Desktop

vectorstrip

Removes vectors from the ends of one or more nucleotide sequences. vectorstrip…

Removes vectors from the ends of one or more nucleotide sequences. vectorstrip writes nucleotide sequences out again but with any of a specified set of vector sequences removed from the 5' and…

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checktrans
Desktop

checktrans

Reports STOP codons and open reading frame (ORFs) statistics of a protein.…

Reports STOP codons and open reading frame (ORFs) statistics of a protein. checktrans reads a protein sequence containing stop characters and writes a statistical report of any ORFs that are greater…

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drVM
Desktop

drVM detect and reconstruct known viral genomes from metagenomes

Allows rapid viral read identification, genus-level read partition, read…

Allows rapid viral read identification, genus-level read partition, read normalization, de novo assembly, sequence annotation and coverage profiling. In drVM, the first two procedures and sequence…

Most Popular Tools

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Bowtie
Desktop

Bowtie

An ultrafast, memory-efficient short read aligner. It aligns short DNA…

An ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a…

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MetaSee
Web

MetaSee

An extendable toolbox to facilitate the interactive visualization of…

An extendable toolbox to facilitate the interactive visualization of metagenomic samples of interests. MetaSee includes: (I) a core visualization engine that is composed of different views for…

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QIIME
Desktop

QIIME Quantitative Insights Into Microbial Ecology

An open source software package for comparison and analysis of microbial…

An open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data.

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Orione
Web

Orione

A Galaxy-based framework consisting of publicly available research software and…

A Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for next-generation sequencing microbiology…

Curators for Metagenomic sequencing analysis

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