List of RNA-Seq bioinformatics tools | Wikipedia audio article
Channel: wikipedia tts
Date: 2019-06-06

This is an audio version of the Wikipedia Article:
https://en.wikipedia.org/wiki/List_of_RNA-Seq_bioinformatics_tools


00:00:32 1 Design
00:01:35 2 Quality control, trimming, error correction and pre-processing of data
00:02:18 2.1 Quality control
00:09:31 2.2 Improving the quality
00:10:35 2.2.1 Trimming and adapters removal
00:19:29 2.2.2 Detection of chimeric reads
00:20:27 2.2.3 Error correction
00:24:33 2.2.4 Bias correction
00:26:34 2.2.5 Other tasks/pre-processing data
00:30:09 3 Alignment tools
00:30:40 3.1 Short (unspliced) aligners
00:37:32 3.2 Spliced aligners
00:38:14 3.2.1 Aligners based on known splice junctions (annotation-guided aligners)
00:40:28 3.2.2 De novo splice aligners
00:49:22 3.2.2.1 De novo splice aligners that also use annotation optionally
00:50:43 3.2.2.2 Other spliced aligners
00:51:04 3.3 Evaluation of alignment tools
00:52:03 4 Normalization, quantitative analysis and differential expression
00:52:16 4.1 General tools
01:14:14 4.2 Evaluation of quantification and differential expression
01:15:54 4.3 Multi-tool solutions
01:16:32 5 Workbench (analysis pipeline / integrated solutions)
01:16:45 5.1 Commercial solutions
01:18:10 5.2 Open (free) source solutions
01:30:06 6 Alternative splicing analysis
01:30:17 6.1 General tools
01:38:49 6.2 Intron retention analysis
01:39:21 6.3 Differential isoform/transcript usage
01:41:35 7 Fusion genes/chimeras/translocation finders/structural variations
01:46:37 8 Copy number variation identification
01:47:12 9 Single cell RNA-Seq
01:50:19 9.1 Integrated Packages
01:51:06 9.2 Quality Control and Gene Filtering
01:51:46 9.3 Normalization
01:52:13 9.4 Dimension Reduction
01:52:32 9.5 Differential Expression
01:53:18 9.6 Clustering
01:53:27 9.7 Pseudo-time Construction
01:53:37 9.8 Visualization
01:53:48 10 RNA-Seq simulators
01:59:42 11 Transcriptome assemblers
02:00:38 11.1 Genome-guided assemblers
02:07:39 11.2 Genome-independent (ide novo/i) assemblers
02:09:55 11.3 Assembly evaluation tools
02:11:32 12 Co-expression networks
02:12:26 13 miRNA prediction and analysis
02:13:31 14 Visualization tools
02:17:59 15 Functional, network and pathway analysis tools
02:23:23 16 Further annotation tools for RNA-Seq data
02:25:26 17 RNA-Seq databases
02:27:20 17.1 Human related
02:29:26 17.2 Single species' RNA-Seq databases
02:32:55 18 External links
02:33:04 18.1 Webinars and presentations



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SUMMARY
=======
RNA-Seq
 is a technique that allows transcriptome studies (see also Transcriptomics technologies) based on next-generation sequencing technologies. This technique is largely dependent on bioinformatics tools developed to support the different steps of the process. Here are listed some of the principal tools commonly employed and links to some important web resources.