Genotyping by sequencing data analysis software tools
Genotyping by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable high throughput genotyping of large numbers of individuals at a large number of SNP markers. The relatively straightforward, robust, and cost-effective GBS protocol is currently being applied in numerous species by a large number of researchers.
Source text:
(Glaubitz et al., 2014) TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One.
Base calling
34 tools
Read quality control
113 tools
Adapter trimming
108 tools
Read clustering
25 tools
Demultiplexing
28 tools
Genome assembly
170 tools
Read alignment
258 tools
Germline SNP detection
157 tools
Somatic SNV detection
101 tools
Sequence homology search
90 tools
Quality control
16 tools
Genotype imputation
40 tools
Summary statistics
27 tools
Single SNP association
45 tools
Fine mapping
12 tools
Region-based association
7 tools
Association mapping
46 tools
Rare variant association
54 tools
Joint association
24 tools
Linkage disequilibrium assessment
28 tools
Haplotype association
21 tools
SNP prioritization
75 tools
Meta-analysis
35 tools
Power/sample size calculation
6 tools
Linkage analysis
71 tools
Bioinformatics workflows
2 tools
