Entering edit mode
12.5 years ago
Istvan Albert
102k
STACKS is a software pipeline for building loci out of a set of short-read sequenced samples. Stacks was developed for the purpose of building genetic maps from RAD-Tag Illumina sequence data, but can also be readily applied to population studies, and phylogeography.
Pipeline components
- ustacks - The unique stacks program will take as input a set of short-read sequences and align them into exactly-matching stacks. Comparing the stacks it will form a set of loci and detect SNPs at each locus using a maximum likelihood framework1.
- cstacks - A catalog can be built from any set of samples processed by the ustacks program. It will create a set of consensus loci, merging alleles together. In the case of a genetic cross, a catalog would be constructed from the parents of the cross to create a set of all possible alleles expected in the progeny of the cross.
- sstacks - Sets of stacks constructed by the ustacks program can be searched against a catalog produced by the cstacks program. In the case of a genetic map, stacks from the progeny would be matched against the catalog to determine which progeny contain which parental alleles.
- pstacks - Similar to ustacks, except this program will extract stacks that have been aligned to a reference genome by a program such as Bowtie and identify SNPs. These stacks can then be processed with cstacks or sstacks to track haplotypes within a population.
Stacks is implemented in C++, with some helper programs in Perl, and is parallelized using the OpenMP libraries. It will compile on GNU-based Linux systems or BSD-based OS X systems. Stacks is released under the GNU GPL license.
So what is the advantage of Stacks over a classic variant pipeline (using gatk, picard etc.)
No answer ?? I'm thinking about using Stacks for a big project but I need more information
Please don't ask new questions in the comment or answer section. This site is built as a Q&A where new questions have to be at top level.
Not sure to understand ... You made advert for your tool, I have the right to ask you some questions ... If you are not able to answer just say you don't know.
Read Istvan's message again. He did not say that you couldn't ask questions. He said that questions should not be attached as comments/answers, but should be submitted as new questions. If you don't know how, see this post.