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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 09:57]
sebastien.renaut
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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) ====
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   * [[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 ====
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   * [[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.