FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
Remarque Citing freebayes: Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012
|Run Unix # freebayes -f [REFERENCE] [OPTIONS] [BAM FILES] >[OUTPUT]||Run Web #|
This is a novel mining pipeline (2009), Integrative Next-generation Genome Analysis Pipeline (inGAP), guided by a Bayesian principle to detect single nucleotide polymorphisms (SNPs), insertion/deletions (indels) by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. inGAP can be applied to the mapping of both Roche/454 and Illumina reads with no restriction of read length.
|Run Unix # inGAP||Run Web #|
Indentify SNPs in a set of genome sequences without the requirement of a reference sequence or a multiple sequence alignment. Reconstruction of SNP based phylogenies by maximum likelihood.
|Run Unix # kSNP -k kmer_length -f fasta -d output_directory [-p genomes4positions_list] [-u unassembled_genomes_list] [-m minimum_fraction_genomes_with_locus] [-G genbank.gbk] [-n num_CPU] [-j ] [-v ] [-c min_kmer_coverage]||Run Web #|
PolyPhred is a program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions.
|Run Unix # polyphred||Run Web #|
TFM-Pvalue is a software suite providing tools for computing the score threshold associated to a given P-value and the P-value associated to a given score threshold. It uses Position Weight Matrices, such as those available in the Transfac or Jaspar databases.
Remarque Efficient and accurate P-value computation for Position Weight Matrices H. Touzet and J.S. Varré Algorithms for Molecular Biology 2007, 2:15
|Run Unix #||Run Web #|
variant detection in massively parallel sequencing data ￼
|Run Unix # varscan [COMMAND] [OPTIONS]||Run Web #|