TopHat 2.0.0 has been released, which can use Bowtie2 (by the default) as well as Bowtie1. The new version is available at
Detailed information and some instructions about TopHat 2.0.0 are as follows:
============================================
TopHat 2.0.0 release 4/09/2012
Version 2.0.0 is a major release adding Bowtie 2 support, better parallelization and the ability to align RNA-Seq reads across potential fusion points.
TopHat now uses Bowtie2 by default (if found in the system) although it can also fall back on Bowtie 1 (which is still required for SOLiD reads).
Bowtie 2 integration features:
most of the optional SAM fields (AS, MD, NM, and etc.) generated by Bowtie 2 are now reported by TopHat as well (reconstructed as necessary)
many of the Bowtie 2 options can now be directly given as TopHat options using --b2-<bowtie option name>. These apply to initial read mappings, not to segment mappings - please see the corresponding manual section.
TopHat 2 maps reads against transcriptome (optional), genome, and novel/known splice sites using Bowtie 2 (or 1) in a fashion meant to increase the overall mapping sensitivity and accuracy. In the case of Bowtie 2, reads poorly mapped in the initial stages (with lower scoring alignments due to indels etc.) will be made available for re-mapping in downstream stages. Alignments obtained in all participating stages are pooled and the best alignments will be finally reported for each read. Please note that this TopHat version requires the installation of Bowtie version 2.0.0-beta5 or later; also note that Bowtie1 and Bowtie2 indexes are different, so it is necessary to use the new Bowtie 2 indexes with TopHat 2 (unless --bowtie1 option is used or bowtie 2 is not found in the system). Since the iGenome Bowtie indexes do not include Bowtie 2 indexes, you may want to download Bowtie 2 indexes from the Bowtie2 website or build them using bowtie2-build.
Most of the time-consuming steps in the TopHat 2 pipeline are now parallelized, reducing the total running time substantially on multi-processor systems.
In addition to mapping across splice sites, TopHat 2 can now align reads across fusion points, which usually occur due to genomic translocations, read-through transcription, or trans-splicing; Tophat 2 integrates the fusion discovery engine previously found in TopHat-Fusion (fusion mapping is optional, please see the separate page for fusion mapping and the --fusion-... options in the manual).
Colorspace (SOLiD) reads require the older version of Bowtie, since Bowtie 2 does not provide support for this kind of reads.
--closure-search and --butterfly-search options have been deprecated
In addition to reporting the best (or primary) alignments (the original TopHat behavior), TopHat 2 can report the secondary alignments up to 20 (the default) paired or single alignments (see --report-secondary-alignments and -g/--max-multihits)
The installation of the Boost package is now required in order to build TopHat 2 from source (see Installation).
New options affecting TopHat's output:
--keep-fasta-order (for those who prefer the order of reference sequences in the SAM output to match the order of the sequences in the genome fasta file)
--report-discordant-pair-alignments
If you had some older versions of TopHat and TopHat-Fusion installed on your system, we suggest that you remove both programs before installing the new version and make sure that your system PATH includes the new version but does not include the other ones.
============================================
Thanks,
Daehwan
Detailed information and some instructions about TopHat 2.0.0 are as follows:
============================================
TopHat 2.0.0 release 4/09/2012
Version 2.0.0 is a major release adding Bowtie 2 support, better parallelization and the ability to align RNA-Seq reads across potential fusion points.
TopHat now uses Bowtie2 by default (if found in the system) although it can also fall back on Bowtie 1 (which is still required for SOLiD reads).
Bowtie 2 integration features:
most of the optional SAM fields (AS, MD, NM, and etc.) generated by Bowtie 2 are now reported by TopHat as well (reconstructed as necessary)
many of the Bowtie 2 options can now be directly given as TopHat options using --b2-<bowtie option name>. These apply to initial read mappings, not to segment mappings - please see the corresponding manual section.
TopHat 2 maps reads against transcriptome (optional), genome, and novel/known splice sites using Bowtie 2 (or 1) in a fashion meant to increase the overall mapping sensitivity and accuracy. In the case of Bowtie 2, reads poorly mapped in the initial stages (with lower scoring alignments due to indels etc.) will be made available for re-mapping in downstream stages. Alignments obtained in all participating stages are pooled and the best alignments will be finally reported for each read. Please note that this TopHat version requires the installation of Bowtie version 2.0.0-beta5 or later; also note that Bowtie1 and Bowtie2 indexes are different, so it is necessary to use the new Bowtie 2 indexes with TopHat 2 (unless --bowtie1 option is used or bowtie 2 is not found in the system). Since the iGenome Bowtie indexes do not include Bowtie 2 indexes, you may want to download Bowtie 2 indexes from the Bowtie2 website or build them using bowtie2-build.
Most of the time-consuming steps in the TopHat 2 pipeline are now parallelized, reducing the total running time substantially on multi-processor systems.
In addition to mapping across splice sites, TopHat 2 can now align reads across fusion points, which usually occur due to genomic translocations, read-through transcription, or trans-splicing; Tophat 2 integrates the fusion discovery engine previously found in TopHat-Fusion (fusion mapping is optional, please see the separate page for fusion mapping and the --fusion-... options in the manual).
Colorspace (SOLiD) reads require the older version of Bowtie, since Bowtie 2 does not provide support for this kind of reads.
--closure-search and --butterfly-search options have been deprecated
In addition to reporting the best (or primary) alignments (the original TopHat behavior), TopHat 2 can report the secondary alignments up to 20 (the default) paired or single alignments (see --report-secondary-alignments and -g/--max-multihits)
The installation of the Boost package is now required in order to build TopHat 2 from source (see Installation).
New options affecting TopHat's output:
--keep-fasta-order (for those who prefer the order of reference sequences in the SAM output to match the order of the sequences in the genome fasta file)
--report-discordant-pair-alignments
If you had some older versions of TopHat and TopHat-Fusion installed on your system, we suggest that you remove both programs before installing the new version and make sure that your system PATH includes the new version but does not include the other ones.
============================================
Thanks,
Daehwan
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