Genotyping from short reads using cloud computing

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Related Tools

    Bowtie: Ultrafast short read alignment
    Hadoop: Open Source MapReduce
    Contrail: Cloud-based de novo assembly
    CloudBurst: Sensitive MapReduce alignment
    Myrna: Cloud, differential gene expression
    Tophat: RNA-Seq splice junction mapper
    Cufflinks: Isoform assembly, quantitation
    SoapSNP: Accurate SNP/consensus calling

Reference jars

    H. sapiens: hg18/dbSNP 130
    M. musculus: mm9/dbSNP 128
    E. coli: O157:H7, NCBI (no SNPs)

Related publications


Other Documentation

  • WABI 09 Poster (.pdf)


News archive

Crossbow on GitHub - 6/11/2013

Version 1.2.1 - May 30, 2013

  • Fixed some failures caused by the new SRA's utilities interface changes.
  • Updated the examples to work with the new SRA interface.
  • Fixed mouse example to properly check crossbow predefined paths if they exists.
  • Changed soapsnp to static linkage to avoid confusion on multilib platforms where user might use alternate LD_LIBRARY_PATH.

Version 1.2.0 - July 20, 2012

  • Added support for Hadoop version 0.20.205.
  • Dropped support for Hadoop versions prior to 0.20.
  • Updated default Hadoop version for EMR jobs to 0.20.205.
  • Updated Bowtie version used to 0.12.8.
  • Fixed issues with streaming jar version parsing.
  • Fixed documentation bugs regarding --sra-toolkit option, which is superseded by the --fastq-dump option.

Version 1.1.2 - May 23, 2011

  • Added --just-align and --resume-align options. --just-align causes Crossbow to put the results of the Alignment phase in the --output directory and quit after the alignment phase. You can later "resume" Crossbow by specifying this directory as the --input directory and specifying the --resume-align option.
  • Fixed issue with .sra input whereby status output from fastq-dump would be interpreted as a read.
  • Other minor bugfixes.

Version 1.1.1 - February 7, 2011

  • Added support for the .sra file format, used by the Sequence Read Archive. These files can now be specified in the manifest. Crossbow uses the fastq-convert tool from the SRA Toolkit to convert .sra files to FASTQ files in the preprocess stage.
  • The examples that included defunct SRA FASTQ files were updated to point to new .sra files instead.

Version 1.1.0 - October 12, 2010

  • Added --discard-ref-bin and --discard-all options, which can be helpful to reduce Crossbow running time when a run's chief purpose is to test whether it runs all the way through.
  • Fixed a bug in soapsnp that caused a segmentation fault in the last partition of a chromosome when chromosome length is a multiple of 64.
  • Revamped the reference jar scripts (in $CROSSBOW_HOME/reftools). The new scripts use Ensembl rather than UCSC & dbSNP. The old scripts (db2ssnp* and *_jar) are still there, but are likely to be deprecated soon.
  • Fixed a few bugs in the hg19_jar and db2ssnp_hg19 scripts.
  • Removed the hg18_jar script, which was broken by a reorganization of the dbSNP site.
  • Uses Bowtie 0.12.7 instead of 0.12.5.
  • Switched Mouse17 example's manifest files back to use .gz extension instead of .bz2.

Version 1.0.9 - September 13, 2010

  • Fixed example manifests that point to Short Read Archive files to use .bz2 instead of .gz extensions.

Version 1.0.8 - September 4, 2010

  • Set the memory cap on the sort task to be inversely proportional to --cpus, to avoid memory footprint blowup on computers with more processors.
  • Fixed a final issue that affected how Crossbow handles quality value conversion.
  • Fixed issue whereby bzip2'ed data would be handled incorrectly by the preprocessor.
  • Fixed counter in Preprocess step that would erroneously refer to unpaired reads as paired. Also "Read data fetched to EC2" has been changed to "Read data fetched".
  • In EMR mode, updated where user credentials are found; Amazon changed their path sometime around 8/30/2010.
  • In EMR mode, updated the manner in which the bootstrap action is specified; the old way was disabled by Amazon sometime around 8/30/2010.
  • Fixed issue whereby would crash in cases with a large number of bins (>10 million) .
  • NOTE: The Short Read Archive (SRA) seems to be in the midst of a reorganization that includes files that were previously gzipped being replaced with versions zipped with bzip2. The files will sometimes disappear for a while. If you are having problems with an example where input reads come from the SRA, try renaming files in the manifest file as appropriate. If that doesn't work, please contact us.

Version 1.0.7 - August 27, 2010

  • Fixed issue whereby the order of the arguments to bowtie would result in a crash when POSIXLY_CORRECT was set.
  • Fixed --keep-all option, which was causing a crash.
  • Fixed a lingering quality bug whereby qualities were converted immediately to phred33 but phred64 or solexa64 flags would be spuriously passed to Bowtie.

Version 1.0.6 - August 26, 2010

  • Single-computer mode now copies the output that it writes to the console to a file cb.local.(pid).out. Please include the contents of this file when reporting issues.
  • Sorting in single-computer mode is now more portable; switched from command-line sort to pure-Perl File::Sort.
  • Fixed bug whereby the quality setting would be propagated to Bowtie but not to SOAPsnp, causing SOAPsnp to operate with incorrect (over-optimistic) quality values when Phred+64 or Solexa+64 modes were used.
  • More helpful output from and to make it easier to debug issues in single-computer-mode runs.
  • Fixed issue where web form would incorrectly convert + signs in AWS secret key to spaces, causing some good credentials to fail verification.
  • Fixed issue in preprocessor that mishandles copies when user's AWS secret key contains slash characters.

Version 1.0.5 - August 16, 2010

  • Fixed issue that prevented CROSSBOW_EMR_HOME environment variable from working.
  • Fixed issue whereby script fails to report a count for the number of reads with alignments sampled due to Bowtie's -M option.
  • Fixed issue whereby scripts in the $CROSSBOW_HOME/reftools directory had #!/bin/sh headers but were actually bash scripts.
  • Fixed issue that made it difficult to specify a space-separated list of arguments to the --bowtie-args and other --*-args parameters.
  • Fixed issue whereby most documentation referred to arguments with a single-dash prefix, whereas users with the POSIXLY_CORRECT environment variable set must use a double-dash prefix. Documentation and code have been updated to always use double-dash prefixes.

Myrna paper out - 8/11/10

Major revision: Version 1.0.4 - July 22, 2010

  • Crossbow has been largely rewritten as an Amazon Elastic MapReduce (EMR) application, as opposed to an Elastic Compute Cloud (EC2) application. EMR runs on top of EC2 and is a more appropriate way to run Crossbow for several reasons, including:
    • The AWS Console's Elastic MapReduce tab, together with EMR's Debug Job Flow feature, provide a much friendlier interface for monitoring and manipulating jobs.
    • The elaborate scripts for automating cluster setup, teardown, proxy connection, etc., that were in old versions of Crossbow are all gone. They are either no longer relevant, or else are handled automatically by EMR.
  • A web-based GUI for composing and submitting EMR jobs has been added. Most helpfully, the web GUI has features for sanity-checking inputs; e.g. whether the user's credentials as entered are valid, whether the input URL exists, etc.
  • Crossbow is now fully "tri-mode", with separate cloud, Hadoop, and single-computer operating modes. All three modes share a great deal of common infrastructure, making all three modes easier to maintain going forward.
    • Crossbow's Hadoop mode is now much improved, having an interface very similar to cloud and single-computer modes.
    • A new single-computer operating mode has been added that (a) uses many processors/cores to shorten computation time, and (b) does not require the user to have a cloud account or a Hadoop installation. It also doesn't require Java; just appropriate versions of Bowtie, SOAPsnp (some of which are included), Perl, and other tools. Its interface is very similar to cloud and Hadoop modes.
  • The manual is entirely rewritten. It now contains information about running in all three modes (cloud, Hadoop, single-computer), and gives multiple examples for how to run in each mode.
  • Fixed a bug whereby allele frequency columns in the provided reference jars had T and G columns switched.
  • SOAPsnp reduce step now outputs more counter and status information.
  • SOAPsnp reduce step outputs an additional column per SNP indicating paired-end coverage.
  • Compatible with Bowtie versions 0.12.0 and above. Bowtie 0.12.5 now included.
  • Compatible with Hadoop 0.18 or 0.20; both were tested.
  • Many other new options and features. See manual.

Crossbow 0.2.0 and Crossbow for Elastic MapReduce - Coming soon

  • Crossbow has been rewritten to allow it to run as an Amazon Elastic MapReduce application. EMR is a much easier and slicker way of running MapReduce programs on EC2. It will also be easier for us to maintain.
  • Fixed a bug whereby allele frequency columns in the provided reference jars had T and G columns switched.
  • SOAPsnp reduce step now outputs more counter and status information.
  • SOAPsnp reduce step outputs an additional column per SNP indicating paired-end coverage.
  • Compatible with Bowtie versions 0.12.0 and above.

Bowtie 0.12.0 - 12/23/09

Crossbow paper out - 11/20/09

0.1.3 release - 10/21/09

  • cb-local now gives the user clear feedback when worker nodes fail to confirm the MD5 signature of the reference jar. If this failure occurs several times per node across all nodes, the supplied MD5 is probably incorrect.
  • An extra Reduce step was added to the end of the Crossbow job to bin and sort SNPs before downloaded to the user's computer. This step also renames output files by chromosome and deletes empty output files.
  • Added another example that uses recently-published mouse chromosome 17 data (sequenced by Sudbery et al). The TUTORIAL file now points to this new example.
  • More and clearer messages in the output from cb-local.

Crossbow piece on Cloudera Blog - 10/15/09

  • Mike Schatz, Crossbow co-author, has a great guest post on Cloudera's "Hadoop & Big Data" blog about Crossbow.

0.1.2 release - 10/13/09

  • Many fixes for the scripts that automate the reference-jar building process.
  • Added two utility scripts, dist_mfa and sanity_check, to the reftools subdirectory. See their documentation for details.
  • Added scripts for building a reference jar for C. elegans using UCSC's ce6 (WormBase's WS190) assembly and information from dbSNP. This small genome is used in the new TUTORIAL.
  • New TUTORIAL steps the user through preprocessing reads from the NCBI Short Read Archive, creating a reference jar from a UCSC assembly (ce6 in this case) and a set of SNP descriptions from dbSNP, then running Crossbow and examining the resulting SNPs.
  • Extended the preprocess-and-copy infrastructure to allow output from a single input file to be split over many output files. This is critical for achieving good load balance across a breadth of datasets.

0.1.1 release - 10/9/09

  • Added scripts that automate the reference-jar building process for UCSC genomes hg18 and mm9. These scripts can be adapted to other species. See the new "Using Automatic Scripts" subsection of the "Building a Reference Jar" section of the MANUAL for details.
  • License agreement files are now organized better. All licenses applying to all software included in Crossbow are in LICENSE* files in the Crossbow root directory.
  • Minor updates to MANUAL

0.1.0 release - 10/3/09

The first public release of Crossbow is now available for download. This release includes:
  • A detailed manual (MANUAL in the expanded archive) that includes step-by-step instructions for how to get started with Amazon Web Services and Crossbow.
  • Scripts for copying and preprocessing short-read FASTQ files into Amazon's S3 storage service, including an easy-to-use interactive script (cb-copy-interactive)
  • Scripts for running Crossbow either locally or on Amazon's EC2 utility computing service, including an easy-to-use interactive script (cb-interactive)