Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
ngs_sequence_alignment_and_variant_calling [2014/11/26 09:57]
sebastien.renaut [Bioinformatics tools geared specifically towards gene expression (RNAseq) analyses]
ngs_sequence_alignment_and_variant_calling [2014/11/26 09:58]
sebastien.renaut [Bioinformatics tools geared specifically towards gene expression (RNAseq) analyses]
Line 30: Line 30:
   * [[http://​bioinf.spbau.ru/​spades|SPADES]] 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) ==== ==== Variant calling (SNPs / short indels) ====
-  
   * [[http://​www.htslib.org/​|samtools]] -Samtools is a suite of programs for interacting with high-throughput sequencing data.   * [[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)]] There are a variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance.   * [[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 ==== ==== 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://​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.   * [[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.
Line 42: Line 40:
 ==== Bioinformatics tools geared specifically towards gene expression (RNAseq) analyses ==== ==== 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    * [[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#R Packages for Genetics and Sequence Analyses|here]] are specifically geared towards gene expression analyses+   * 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 ==== ==== All-in-one proprietary software ====
   * [[http://​www.geneious.com/​|geneious]] ​ -Comprehensive bioinformatics software platform.   * [[http://​www.geneious.com/​|geneious]] ​ -Comprehensive bioinformatics software platform.