Differences
This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision | ||
ngs_sequence_alignment_and_variant_calling [2014/11/17 13:09] sebastien.renaut [Microbial diversity / ecology] |
ngs_sequence_alignment_and_variant_calling [2014/11/26 09:58] (current) sebastien.renaut [Bioinformatics tools geared specifically towards gene expression (RNAseq) analyses] |
||
---|---|---|---|
Line 11: | Line 11: | ||
==== Data manipulation ==== | ==== 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://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 ==== | ==== 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. | * [[https://www.broadinstitute.org/gatk/|The Genome Analysis Toolkit (GATK)]] -Software package developed at the Broad Institute to analyze high-throughput sequencing data. | ||
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)]] | + | * [[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|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. | ||
Line 54: | Line 52: | ||
==== Microbial diversity / ecology ==== | ==== 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://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 |