Team III Functional Annotation Group: Difference between revisions
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=='''Results'''== | =='''Results'''== | ||
===''' | ==='''CARD-RGI'''=== | ||
$ | $ rgi -i <input_file> -o <output_file> | ||
[[File: | [[File: CARD-RGI.PNG]] | ||
===''' | ==='''VFDB'''=== | ||
$ | $ makeblastdb -in <input_db> -parse_seqids -blastdb_version 5 -dbtype nucl -out <name_db> | ||
[[File: | $ blastn -db <name_db> -query <input_file> -out <output_file> -max_hsps 1 -max_target_seqs 1 -num_threads 4 -evalue 1e-5 | ||
[[File: VFDB.PNG]] | |||
===''' | ==='''PILERCR'''=== | ||
$ | $ ./pilercr -in <input_file> -out <output_file> | ||
[[File: | [[File: Piler-cr.PNG]] | ||
=='''References'''== | =='''References'''== | ||
Revision as of 19:25, 9 April 2020
Group Members - Allison, Bengu, Cheng, Pallavi Misra
Introduction
Initial Pipeline
Homology Tools
CARD-RGI
VFDB
Ab-initio - Tools
PILERCR
Final Pipeline
Results
CARD-RGI
$ rgi -i <input_file> -o <output_file>
VFDB
$ makeblastdb -in <input_db> -parse_seqids -blastdb_version 5 -dbtype nucl -out <name_db> $ blastn -db <name_db> -query <input_file> -out <output_file> -max_hsps 1 -max_target_seqs 1 -num_threads 4 -evalue 1e-5
PILERCR
$ ./pilercr -in <input_file> -out <output_file>
