The document discusses creating a pipeline for EST analysis by assembling EST reads into contigs, detecting SNPs, and displaying results online. Several tools are proposed, including MIRA for assembly but it is noted to be slow, poorly documented, and buggy. The pipeline will parse outputs from tools like BLAST, PFAM, and ORF prediction into a structured database. It has created the pipeline, started analyzing data and filling the database, and next steps are to wait for MIRA and add an SNP parser.
40. What we‘ve got here:
•Different tools
•many different output-files
41. What we‘ve got here:
•Different tools
•many different output-files
What we want:
a structured database containing all the
information
42. How to parse
Class «Parser»
•Function BLAST-Parser
•Function PFAM-Parser
•Function FASTA-Parser
•...
Data
Script
•read input
•use parser
•insert db
43. How to parse
Class «Parser»
•Function BLAST-Parser
•Function PFAM-Parser
•Function FASTA-Parser
•...
Data
Script
•read input
•use parser
•insert db
44. How to parse
Class «Parser»
•Function BLAST-Parser
•Function PFAM-Parser
•Function FASTA-Parser
•...
Data
Script
•read input
•use parser
•insert db
45. How to parse
Class «Parser»
•Function BLAST-Parser
•Function PFAM-Parser
•Function FASTA-Parser
•...
Data
Script
•read input
•use parser
•insert db
46. How to parse
Data
Class «Parser»
•Function BLAST-Parser
•Function PFAM-Parser
•Function FASTA-Parser
•... Script
•read input
•use parser
•insert db
Database
53. Summary & Results
•created the pipeline
•analysed data
•started filling the database
To be done
•wait for MIRA
•SNP-parser
54. thx to:
•Marvin, for «time till scooter» and sending us to Lothar
•Lothar, for providing always friendly and calm advice
•Suse, for actually having used MIRA at least once
•Andrew, for Andreas
•Andreas, for Andrew
•Bastien Chevreux, for not fixing those damn bugs in MIRA
