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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] (current) sebastien.renaut [Bioinformatics tools geared specifically towards gene expression (RNAseq) analyses] |
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| * [[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. | ||
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| ==== 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. | ||
