Differences

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--- ngs_sequence_alignment_and_variant_calling [2014/11/07 16:44]
sebastien.renaut [Variant calling]
+++ ngs_sequence_alignment_and_variant_calling [2014/11/26 14:58] (current)
sebastien.renaut [Bioinformatics tools geared specifically towards gene expression (RNAseq) analyses]
@@ Line 1: / Line 1: @@
-====== Bioinformatics tools for analyzing Next-Generation-Sequencing Data======
+====== Bioinformatics Tools for Analyzing High Throughput Sequencing (NGS) Data======
--This is a (non-exhaustive) list of tools commonly used in bioinformatics analyses of NGS dataset. Although, a lot of these tools can be used for other purposes too (such as microarray data, Sanger sequencing, proteomics).
+  * Commonly used tools in bioinformatics analyses of NGS dataset. Although, a lot of these tools can be used for other purposes too (such as microarray data, Sanger sequencing, proteomics).
--Most of these tools are open source and free.
+  * This is a (non-exhaustive) list, but represents some of the most up-to-date and most commonly used tools.
--Most of these tools are manipulated from the command line, although some of them also provide a GUI (**G**raphical **U**ser **I**nterface).
+  * Most of these tools are open source and free.
+  * Most of these tools are manipulated from the command line, although some of them also provide a GUI (**G**raphical **U**ser **I**nterface).
 ==== Keeping up to data with sequencing platforms and cost ====
   * [[http://www.molecularecologist.com/next-gen-fieldguide-2014/|Next Generation Field Guide by Travis Glenn]] -Originally published in 2011 in [[http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2011.03024.x/abstract;jsessionid=A90E6AD25AB3AD7E1D9FA6D5729C685B.f03t03|Molecular Ecology Resources]], but kept up to date every year. Thorough review of current sequencers, costs, pros and cons.
+==== Data manipulation ====
+  * [[http://broadinstitute.github.io/picard/|Picard Tools]] A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
+  * [[http://www.bioinformatics.babraham.ac.uk/projects/fastqc/|FASTQC]] A quality control tool for high throughput sequence data.
 ==== Sequence alignment ====
   * [[https://www.broadinstitute.org/gatk/|The Genome Analysis Toolkit (GATK)]] -Software package developed at the Broad Institute to analyze high-throughput sequencing data.
@@ Line 17: / Line 21: @@
   * [[http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss|Trans-ABySS]] -de novo assembly of RNA-Seq data using ABySS
   * [[http://soap.genomics.org.cn/SOAPdenovo-Trans.html|SOAPdenovo-Trans]] -de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts
+  * [[http://sourceforge.net/projects/mira-assembler/|MIRA]] -dSequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data.
 ==== de novo genome assembly ====
   * [[http://sourceforge.net/projects/soapdenovo2/|soapdenovo2]] Short-read assembly method that can build a de novo draft assembly for human-sized genomes.
   * [[https://www.ebi.ac.uk/~zerbino/velvet/Velvet]] -A sequence assembler for very short reads.
   * [[http://www.bcgsc.ca/platform/bioinfo/software/abyss|abyss]] -**A**ssembly **By** **S**hort **S**equences - a de novo, parallel, paired-end sequence assembler
+  * [[http://sourceforge.net/projects/mira-assembler/|MIRA]] -dSequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data.
+  * [[http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/|IDBA-UD] for plastid reads, dealing quite well with uneven coverage
+  * [[http://bioinf.spbau.ru/spades|SPADES]] for plastid reads, dealing quite well with uneven coverage
 ==== Variant calling (SNPs / short indels) ====
   * [[http://www.htslib.org/|samtools]] -Samtools is a suite of programs for interacting with high-throughput sequencing data.
-  * [[https://www.broadinstitute.org/gatk/|The Genome Analysis Toolkit (GATK)]]
+  * [[https://www.broadinstitute.org/gatk/|The Genome Analysis Toolkit (GATK)]] There are a variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance.
 ==== Bioinformatics tools geared specifically towards GBS and RAD data ====
   * [[http://sourceforge.net/projects/tassel/|tassel]] -TASSEL is a bioinformatics software package that can analyze diversity for sequences, SNPs, or SSRs.
   * [[http://creskolab.uoregon.edu/stacks/|stacks]] -Software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
   * [[https://github.com/dereneaton/pyrad/releases|pyRAD]] -pyRAD can analyze RAD, ddRAD, GBS, paired-end ddRAD and paired-end GBS data sets.
+==== Bioinformatics tools geared specifically towards gene expression (RNAseq) analyses ====
+   * [[http://ccb.jhu.edu/software/tophat/index.shtml|tophat]] -Aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. Usefull for analysing splice variants and their expression from NGS datasets
+   * There are also several R packages listed [[http://qcbs.ca/wiki/resources_for_r|here]] are specifically geared towards gene expression analyses
 ==== All-in-one proprietary software ====
   * [[http://www.geneious.com/|geneious]]  -Comprehensive bioinformatics software platform.
@@ Line 45: / Line 52: @@
 ==== Microbial diversity / ecology ====
+  * See also [[http://qcbs.ca/wiki/guide_to_amplicon_sequencing_experiment|this]] page on the wiki.
   * [[http://www.mothur.org/wiki/Main_Page|mothur]]  -A comprehensive bioinformatics software platform for microbial ecology (eg. 16S rRNA gene sequences diversity)
-   * [[http://qiime.org/Quantitative Insights Into Microbial Ecology (Qiime)]] -Another comprehensive bioinformatics software platform for microbial ecology  primarily based on high-throughput amplicon sequencing data (such as SSU rRNA). Also has a GUI.
+   * [[http://qiime.org/|Quantitative Insights Into Microbial Ecology (Qiime)]] -Another comprehensive bioinformatics software platform for microbial ecology  primarily based on high-throughput amplicon sequencing data (such as SSU rRNA). Also has a GUI.
+=== Others ===
+  * [[http://weizhong-lab.ucsd.edu/cd-hit/|cd-hit]] Clustering and comparing protein or nucleotide sequences