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39 Free RNA-seq Pre-analysis Tools - Software and Resources

39 Free RNA-seq Pre-analysis Tools - Software and Resources


Quality Control and Assessment of RNA-seq Data

RNA-seq Filtering and Trimming Tools

  1. NGS QC Toolkit
    • Description : NGS QC Toolkit is for quality control and filtering of Roche 454 and Illumina sequencing data. The toolkit also contains functions for sequence format conversion, trimming, and generation of sequence quality statistics.
  2. HTQC
    • Description : HTQC (High-Throughput Quality Control) is a tool for quality control of Illumina sequencing data. The package also contains functions for filtering and generation of graphical reports.
  3. PRINSEQ
    • Description : PRINSEQ is a tool for quality control of metagenomic sequence data. The PRINSEQ includes functions for summary statistics, such as read length, GC content, sequence complexity, quality score distributions, count of duplicate reads, Ns, and poly-A tails, assembly quality measures, and tag sequences. The package also contains functions for trimming, filtering, and data reformatting.
  4. Trimmomatic
    • Description : Trimmomatic is a tool for trimming Illumina sequenced data reads.
  5. fastp
    • Description : fastp is a FASTQ data pre-processing tool. The algorithm has functions for quality control, trimming of adapters, filtering by quality, and read pruning. It also supports multi-threading. The Authors claim fastp to be faster than other FASQ pre-processing tools.
  6. AfterQC
    • Description : AfterQC is a tool for quality control of FASTQ data produced by HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq, and Illumina 1.8 or newer. The algorithm has functions for trimming, filtering, and error correction. It also produces a report in HTML format. The Authors have re-implemented this tool in C++ as "fastp." See links.
  7. QC-Chain
    • Description : QC-Chain is a tool for the quality of high-throughput sequencing data. The package has functions for quality assessment, trimming, and filtering. The Authors have optimized the QC-Chain algorithm for parallel computation. The download link is currently down. The Authors have implemented another tool, RNA-QC-chain (see links), based on the QC-Chain.
  8. RNA-QC-chain
    • Description : RNA-QC-Chain is an RNA-seq quality control tool, based on QC-Chain. The package has functions for quality assessment, trimming, filtering of ribosomal contamination, and reporting.
  9. BIGpre
    • Description : BIGpre is a tool to assess the quality of Illumina and 454 sequencing data. The BIGpre algorithm contains functions for correlation of forward and reverse sequenced reads, GC content, read quality, trimming, and filtering. It produces graphics by integrating R.
  10. FASTX-Toolkit
    • Description : FASTX-Toolkit consists of a collection of tools for pre-processing data from FASTA and FASTQ files. The FASTX-Toolkit includes the following tools (not maintained): 1. FASTQ-Statistics, 2. FASTQ-Quality-BoxPlot, 3. FASTQ-Nucleotides-Distribution (charts), 4. FASTQ-Quality-Converter, 5. FASTQ-Quality-Filter, 6. FASTX-Artifacts-Filter, 7. FASTX-Barcode-Splitter, 8. FASTX-Clipper, 9. FASTA-Clipping-Histogram, 10. FASTX-Reverse-Complement, and 11. FASTX-Trimmer.
  11. ClinQC
    • Description : ClinQC is a pipeline tool to pre-process sequencing data from Sanger, 454, and Ion Torrent platforms. ClinQC has functions for format conversion, quality control, trimming, filtering, and reporting.
  12. ConDeTri
    • Description : ConDeTri is a tool to filter sequencing errors and trim Illumina RNA-seq and DNA sequencing data.
  13. QuasR
    • Description : QuasR is a tool to quantify and annotate reads from RNA-seq, ChIP-seq, and Bis-seq. The QuasR package has tools for all analysis steps from sequence read preprocessing, alignment, and quality control to quantification.

RNA-seq Trimming Tools

  1. cutadapt
    • Description : Cutadapt is a tool for quality control of high-throughput sequencing reads. The functions include an adapter, primer, and poly-A tail removal.
  2. cutadapt-IP
    • Description : Cutadapt-IP is web-based a tool at Galaxy Pasteur to remove adapters, primers, and poly-A tails from high-throughput sequencing reads.
  3. cutPrimers
    • Description : cutPrimers is a tool for removing primers from high-throughput sequencing reads.
  4. SolexaQA
    • Description : SolexaQA is a tool for quality control of Illumina, Ion Torrent, and 454 sequencing data. The functions include visualization of data quality, trimming of low-quality data, and sorting reads based on sequencing quality. The tool runs both on single-end and paired-end data.
  5. QTrim
    • Description : QTrim is a tool for trimming sequence reads based on Phred quality values. The download link is not currently working but if you are interested in obtaining the tool, email the Authors and request if QTrim is still available.
  6. FastqPuri
    • Description : FastqPuri is a pre-processing tool for RNA-seq data. It removes adapter sequences and generates data quality reports and works for both single- and paired-end data.
  7. ngShoRT
    • Description : ngShoRT is a pre-processing tool for trimming high-throughput sequencing data. The ngShoRT algorithm can process both single- and paired-end data and supports multi-threading.
  8. Rbowtie2
    • Description : Rbowtie2 is an R tool that wraps the Bowtie 2 tool and includes adapter removal, read merging and identification.
  9. Rbowtie
    • Description : This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use QuasR instead of using this package directly.
  10. Skewer
    • Description : Skewer is a tool to trim sequence adapters of Illumina paired-end sequencing data.

RNA-seq Filtering Tools

  1. TRAPR
    • Description : A tool for visualization and statistical analysis of RNA-seg data. The TRAPR algorithm can filter low-quality data, normalize, transform, perform statistical analyses, and visualize data. The ability to visualize results supports the creation of customized computing pipelines. It additionally has functions for data management.
  2. umis
    • Description : A tool for expression estimation in RNA-seq tagged data. The umis package includes tools for read formatting, barcode filtering, pseudo-mapping to cDNAs, and counting molecular identifiers.
  3. scater
    • Description : An R package for pre-processing, quality control, expression normalization, and visualization of single-cell RNA-seq data. The scater algorithm includes a suite of plotting functions.

RNA-seq Reporting/Visualization Tools

  1. TRAPR
    • Description : A tool for visualization and statistical analysis of RNA-seg data. The TRAPR algorithm can filter low-quality data, normalize, transform, perform statistical analyses, and visualize data. The ability to visualize results supports the creation of customized computing pipelines. It additionally has functions for data management.
  2. scater
    • Description : An R package for pre-processing, quality control, expression normalization, and visualization of single-cell RNA-seq data. The scater algorithm includes a suite of plotting functions.
  3. FastQC
    • Description : A tool for raw high-throughput sequencing data. The FastQC provides summary graphs and tables.
  4. FQC Dashboard
    • Description : FQC Dashboard is a quality control tool that integrates the results from the FastQC tool (see links) and displays them in an interactive HTML format.
  5. HTQC
    • Description : HTQC (High-Throughput Quality Control) is a tool for quality control of Illumina sequencing data. The package also contains functions for filtering and generation of graphical reports.
  6. PRINSEQ
    • Description : PRINSEQ is a tool for quality control of metagenomic sequence data. The PRINSEQ includes functions for summary statistics, such as read length, GC content, sequence complexity, quality score distributions, count of duplicate reads, Ns, and poly-A tails, assembly quality measures, and tag sequences. The package also contains functions for trimming, filtering, and data reformatting.
  7. SolexaQA
    • Description : SolexaQA is a tool for quality control of Illumina, Ion Torrent, and 454 sequencing data. The functions include visualization of data quality, trimming of low-quality data, and sorting reads based on sequencing quality. The tool runs both on single-end and paired-end data.
  8. AfterQC
    • Description : AfterQC is a tool for quality control of FASTQ data produced by HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq, and Illumina 1.8 or newer. The algorithm has functions for trimming, filtering, and error correction. It also produces a report in HTML format. The Authors have re-implemented this tool in C++ as "fastp." See links.
  9. FastqPuri
    • Description : FastqPuri is a pre-processing tool for RNA-seq data. It removes adapter sequences and generates data quality reports and works for both single- and paired-end data.
  10. RNA-QC-chain
    • Description : RNA-QC-Chain is an RNA-seq quality control tool, based on QC-Chain. The package has functions for quality assessment, trimming, filtering of ribosomal contamination, and reporting.
  11. FQStat
    • Description : FQStat is a tool for the quality assessment of FASTQ data files. The FQStat runs on multiples cores and computes statistics, such as read counts, lengths, and quality scores, separately for lane, sample, and experiment. FQStat also tags low-quality data and works on both paired- and single-end data.
  12. PIQA
    • Description : PIQA is a tool for computing statistics for Illumina G1 sequencing data, such as tile-by-tile and cycle-by-cycle, cluster density, quality, and nucleotide frequencies.
  13. BIGpre
    • Description : BIGpre is a tool to assess the quality of Illumina and 454 sequencing data. The BIGpre algorithm contains functions for correlation of forward and reverse sequenced reads, GC content, read quality, trimming, and filtering. It produces graphics by integrating R.
  14. htseq-qa
    • Description : htseq-qa tool is for quality assessment of RNA-seq data. It creates plots of positional nucleotide compositions and quality values. It is a part of the HTSeq package (see links).
  15. FASTX-Toolkit
    • Description : FASTX-Toolkit consists of a collection of tools for pre-processing data from FASTA and FASTQ files. The FASTX-Toolkit includes the following tools (not maintained): 1. FASTQ-Statistics, 2. FASTQ-Quality-BoxPlot, 3. FASTQ-Nucleotides-Distribution (charts), 4. FASTQ-Quality-Converter, 5. FASTQ-Quality-Filter, 6. FASTX-Artifacts-Filter, 7. FASTX-Barcode-Splitter, 8. FASTX-Clipper, 9. FASTA-Clipping-Histogram, 10. FASTX-Reverse-Complement, and 11. FASTX-Trimmer.
  16. ClinQC
    • Description : ClinQC is a pipeline tool to pre-process sequencing data from Sanger, 454, and Ion Torrent platforms. ClinQC has functions for format conversion, quality control, trimming, filtering, and reporting.
  17. QuasR
    • Description : QuasR is a tool to quantify and annotate reads from RNA-seq, ChIP-seq, and Bis-seq. The QuasR package has tools for all analysis steps from sequence read preprocessing, alignment, and quality control to quantification.

Other Pre-analysis RNA-seq Tools

  1. umis
    • Description : A tool for expression estimation in RNA-seq tagged data. The umis package includes tools for read formatting, barcode filtering, pseudo-mapping to cDNAs, and counting molecular identifiers.
  2. RVboost
    • Description : RVboost is a tool for prioritizing RNA-seq variants. The RVboost algorithm uses characteristics that are uniques to RNA library preparation and sequencing. RVboost utilizes a boosting method to train models using variants stored in HapMap. The RVboost consists of a workflow combining variant calling, filtering, and annotation.
  3. DNABarcodes
    • Description : DNABarcodes is a tool for creating DNA barcodes for the purpose of error correction. The DNABarcodes algorithm can analyze existing barcodes by determining their distances.
  4. VDJPipe
    • Description : VDJPipe is a tool to pre-process immune repertoire sequencing data. The VDJPipe package includes functions for base composition statistics the calculation, read quality statistics calculation, quality filtering, homopolymer filtering, length, and nucleotide filtering, paired-read merging, barcode demultiplexing, 5' and 3' PCR primer matching, and duplicate reads collapsing.
  5. trumpet
    • Description : trumpet is a tool for the quality assessment of m(6)A-seq data. The trumpet algorithm combines the quality metrics of both ChIP-seq and RNA-seq.
  6. NGS QC Toolkit
    • Description : NGS QC Toolkit is for quality control and filtering of Roche 454 and Illumina sequencing data. The toolkit also contains functions for sequence format conversion, trimming, and generation of sequence quality statistics.
  7. AfterQC
    • Description : AfterQC is a tool for quality control of FASTQ data produced by HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq, and Illumina 1.8 or newer. The algorithm has functions for trimming, filtering, and error correction. It also produces a report in HTML format. The Authors have re-implemented this tool in C++ as "fastp." See links.
  8. gdc-rnaseq-tool
    • Description : gdc-rnaseq-tool for retrieving RNA-seq files from the GDC portal that are identified by TCGA barcodes.
  9. Rbowtie2
    • Description : Rbowtie2 is an R tool that wraps the Bowtie 2 tool and includes adapter removal, read merging and identification.
  10. Rbowtie
    • Description : This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use QuasR instead of using this package directly.
  11. NGSQC
    • Description : NGSQC (Next Generation Sequencing Quality Control) is a pipeline tool for quality control of SOLiD platform sequencing data.
  12. FASTX-Toolkit
    • Description : FASTX-Toolkit consists of a collection of tools for pre-processing data from FASTA and FASTQ files. The FASTX-Toolkit includes the following tools (not maintained): 1. FASTQ-Statistics, 2. FASTQ-Quality-BoxPlot, 3. FASTQ-Nucleotides-Distribution (charts), 4. FASTQ-Quality-Converter, 5. FASTQ-Quality-Filter, 6. FASTX-Artifacts-Filter, 7. FASTX-Barcode-Splitter, 8. FASTX-Clipper, 9. FASTA-Clipping-Histogram, 10. FASTX-Reverse-Complement, and 11. FASTX-Trimmer.
  13. ClinQC
    • Description : ClinQC is a pipeline tool to pre-process sequencing data from Sanger, 454, and Ion Torrent platforms. ClinQC has functions for format conversion, quality control, trimming, filtering, and reporting.
  14. PrimerSeq
    • Description : PrimerSeq is a tool to design RT-PCR primers for the evaluation of alternative splicing using RNA-seq data.
  15. Rcorrector
    • Description : Rcorrector is a tool to correct Illumina platform sequencing errors in RNA-seq datasets. The Rcorrector algorithm is based on k-mers and De Bruhin graphs.
  16. htSeqTools
    • Description : htSeqTools is an R package to process, quality control, and visualize RNA-seq and ChIP-seq datasets. The package includes MDS plots, detection of amplification artifacts, functions for the identification of high coverage genomic regions, and visualization of coverage profiles.





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