Welcome to the Computational Research and Development Group (CRD) homepage. We are part of the Genome Sequencing and Analysis Program at the Broad Institute. This site presents research tools we have developed for working with genome sequence data, and which we provide support for. If you have any trouble using them, please check our general help first, then write to us at crdhelp@broadinstititute.org.

These tools are the computational part of the solution to two general problems, how to find the sequence of a genome, and how to find the differences between the sequences of two genomes.

Do you want the sequence of a genome?

We have been sequencing and assembling genomes since before 2000. Our goal is to produce high-quality draft sequences at low cost. To do this, we look for the optimal deployment of cutting-edge sequencing technologies and assembly algorithms. Here we describe the two laboratory and computational strategies that we are presently pursuing, and then the software packages for assembly that we have developed.

METHODS FOR VERY SHORT READS.

We have developed and tested a method for assembling very short (~30 base) paired reads using the ALLPATHS algorithm. This method requires high coverage from two libraries, one from fragments of size 3-4 kb, and one from shorter fragments.

METHODS FOR SHORT READS.

Because very short reads may be inadequate for large genomes, and because next generation sequencing technologies are starting to produce longer reads, we are exploring a strategy that applies the ALLPATHS algorithm to the following data:

• 100 base reads from 180 bp ± 10% fragments, 45x coverage
• 100 base reads from ~3000 bp ± 10% fragments, 45x coverage
• additional sequence from longer fragments for large genomes.

Such data are starting to become available on the Illumina platform. At 90x total coverage, the cost is roughly six-fold lower than the best available alternative, 15x coverage on the 454 platform. However, costs may change rapidly and we will update the strategy accordingly.

• ALLPATHS (download) is a whole genome shotgun assembler that can generate high quality assemblies from short reads. Assemblies are presented in a graph form that retains ambiguities, such as those arising from polymorphism, thereby providing information that has been absent from previous genome assemblies. Our first release (ALLPATHS v1) works with simulated data only, while our second release (ALLPATHS v2) works with real data and has been tested with Illumina reads and on small genomes up to 40 Mb. Our latest release (ALLPATHS v3) is able to assemble large genomes (up to mammalian size) using the latest 100+ base paired Illumina reads. All three versions are available to download along with examples.

  Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. May, 2008. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Research 18(5):810 - 20.

  Maccallum I, Przybylski D, Gnerre S, Burton J, Shlyakhter I, Gnirke A, Malek J, McKernan K, Ranade S, Shea TP, Williams L, Young S, Nusbaum C, Jaffe DB. October 2009. ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biology 1;10(10):R103.

• ARACHNE (download, wiki) was our first genome assembly program. It was designed for long reads from Sanger-method sequencing. It has been used to assemble many genomes, including those that are large and highly repetitive.

  Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. January, 2002. ARACHNE: a whole-genome shotgun assembler. Genome Research 12: 177 - 189.

  Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. January, 2003. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Research 13: 91 - 96.

Do you want the differences between genomes?

We have developed three programs for finding the differences between genomes:

• SWAP454 (download, manual) is a program for calling SNPs using 454 read data. SWAP454 also includes code for creating improved quality scores for 454 read data that has been incorporated into the algorithm used by 454 Life Sciences.

  Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, Russ C, Lander ES, Nusbaum C, Jaffe DB. May, 2008. Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Research 18: 763 - 770.
  

• VAAL (download, manual) VAAL is a variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex genetic variants. On bacterial data sets, it achieves very high sensitivity, and near perfect specificity. VAAL can be used to compare reads from one strain to a reference sequence from another strain. It can also be used to compare reads from two strains to each other, using a third strain to determine homology. For example, we have used VAAL to find a single mutation responsible for bacterial resistance: the output of the program was that single mutation and no others. VAAL uses an assisted assembly algorithm that borrows from ALLPATHS.

  Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, Warren RM, Hung DT, Birren BW, Lander ES, Jaffe DB. Jan 2009. Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nature Methods 6(1):67-9.

• SomaticCall (download, manual) SomaticCall is a program that finds single-base differences (substitutions) between sequence data from tumor and matched normal samples. It takes as input a BAM file for each sample, and produces as output a list of differences (somatic mutations).

General Guidelines

General guidelines on system and software requirements, and instructions for building our software may be found here.