CoReMicrob: Computational Resources for Micorbiome

Major tools for Quality Control of metagenomic reads

This page provides information regarding Major tools for Quality Control of metagenomic reads, along with links to their websites.

Major tools for low quality read removal of metagenomic data

Tool Name Description PubMed ID
FastP A tool designed to provide ultrafast all-in-one preprocessing and quality control for FastQ data. 38868435
FastQC A quality control tool for high throughput sequence data. NA
LongQC A Quality Control Tool for Third Generation Sequencing Long Read Data. 32041730
MultiQC Summarize analysis results for multiple tools and samples in a single report. 27312411
MinIONQC A fast and simple quality control for MinION sequencing data. 30052755
proovread A large-scale high-accuracy PacBio correction through iterative short read consensus. 25015988
SequelTools A suite of tools for working with PacBio Sequel raw sequence data. 33004007
SOAPnuke A MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. 29220494
Trimmomatic A flexible trimmer for Illumina sequence data. 24695404
Cutadapt Removes adapter sequences from high-throughput sequencing reads. EMBnet

Major tools for contamination removal from short-reads

Tool Name Description PubMed ID
BWA Fast and accurate short read alignment with Burrows-Wheeler transform. 19451168
Minimap2 Pairwise alignment for nucleotide sequences. 29750242
Bowtie2 Fast gapped-read alignment. 22388286
STAR Ultrafast universal RNA-seq aligner. 23104886
HISAT2 Graph-based genome alignment and genotyping. 31375807

Major tools for Chimera Removal from meatgenomic reads

Tool Name Description PubMed ID
UCHIME A widely-used tool for detecting chimeric sequences. 21700674
ChimeraSlayer A tool specifically designed for chimera detection in 16S rRNA gene sequences. 21212162
DECIPHER A search-based approach to chimera identification for 16S rRNA sequences. 22101057
s