software for Genome analysis
Budget: ₹1,500 – ₹12,500 INR
Specification of software for Genome analysis
Single, integrated platform solution.
2
U1 (user-interface) solution with no command-line inputs.
3
Support raw data from the following sequencing platforms:
Illumina, 454 (Roche), ABl, Ion Torrent, Pac Bio with multiple library layout formats and
support for VM barcodingOxford Nanopore.
4
Capable of supporting the following workflows and applications:
RA-Seq DNA-Seq-ChIP-Seq Methyl-Seq MeDIP-Seq Small RNA-Seq Multi-Omics
analysis>support for simultaneous analysis of multiple workflows.
5. Provide for U1-hased parameter customizability for all algorithms.
6
Capable of handling: Short reads, long reads, Arbitrary gaps/mis-matches, single-end reads, paired-
end reads
7
Support local realignment, split-read alignment (for detecting long InDels, translocations), Base
Quality Score Recalibration (BQSR).
8
Support analysis for: clustering. PCA,
9
Support integration with R and python including running custom R/py scripts.
10. Efficiently store and compactly manage the analysis data generated
11. Support multiple organisms including non-model organisms &xenograft models.
12. Support entire analysis pipeline- including primary analysis (raw read alignment and corresponding
QC filters), secondary analysis (import of aligned data and corresponding QC filters) and
downstream tertiary analysis like GO, GSEA, Pathways
13. Support data overlay on Pathways, including Wiki-Pathways
14. Have rich, interactive visualizations including gene-level views, variant views, copy number views
15. Have an integrated genome browser, capable of visualizing large stretches of the genome, across
multiple chromosomes (for gene fusion events), at multiple zoom levels
16. Support configurable pipeline creation for standard tasks (e.g. alignment, SNO deteetion etc.)
17. Supported on the following operating systems (64-bit): Windows, Mac, Linux
18. License for single user for 2 years
19. Online/physical support during all working hrs for troubleshoot.
20. Service and support team should be located in India.
Single, integrated platform solution.
2
U1 (user-interface) solution with no command-line inputs.
3
Support raw data from the following sequencing platforms:
Illumina, 454 (Roche), ABl, Ion Torrent, Pac Bio with multiple library layout formats and
support for VM barcodingOxford Nanopore.
4
Capable of supporting the following workflows and applications:
RA-Seq DNA-Seq-ChIP-Seq Methyl-Seq MeDIP-Seq Small RNA-Seq Multi-Omics
analysis>support for simultaneous analysis of multiple workflows.
5. Provide for U1-hased parameter customizability for all algorithms.
6
Capable of handling: Short reads, long reads, Arbitrary gaps/mis-matches, single-end reads, paired-
end reads
7
Support local realignment, split-read alignment (for detecting long InDels, translocations), Base
Quality Score Recalibration (BQSR).
8
Support analysis for: clustering. PCA,
9
Support integration with R and python including running custom R/py scripts.
10. Efficiently store and compactly manage the analysis data generated
11. Support multiple organisms including non-model organisms &xenograft models.
12. Support entire analysis pipeline- including primary analysis (raw read alignment and corresponding
QC filters), secondary analysis (import of aligned data and corresponding QC filters) and
downstream tertiary analysis like GO, GSEA, Pathways
13. Support data overlay on Pathways, including Wiki-Pathways
14. Have rich, interactive visualizations including gene-level views, variant views, copy number views
15. Have an integrated genome browser, capable of visualizing large stretches of the genome, across
multiple chromosomes (for gene fusion events), at multiple zoom levels
16. Support configurable pipeline creation for standard tasks (e.g. alignment, SNO deteetion etc.)
17. Supported on the following operating systems (64-bit): Windows, Mac, Linux
18. License for single user for 2 years
19. Online/physical support during all working hrs for troubleshoot.
20. Service and support team should be located in India.