Table 1. Components developed for EGene pipeline generation system. By convention, component names have two parts: the prefix, stating the component function, and the suffix, stating the third-party software used, when appropriate.  

Component	Third party software required	Function
assemble_cap3.pl	CAP3	Creates a directory structure, runs CAP3 and analyzes redundancy
assemble_phrap.pl	Phrap	Creates a directory structure, runs Phrap and analyzes redundancy
bigou.pl	-	Initializes and runs the pipeline
filter_blast.pl	BLAST	Marks as invalid the sequences with a significant alignment block obtained with BLAST against a specified database
filter_cross_match.pl	Cross_match	Marks as invalid the sequences with a significant alignment block obtained with Cross_match
filter_quality.pl	-	Marks as invalid the sequences not attaining a set of minimum quality criteria
filter_size.pl	-	Marks as invalid the sequences below a threshold size
mask_cross_match.pl	Cross_match	Masks sequence blocks with significant Cross_match alignments against a database
outsave.pl	-	Produces a snapshot of all sequences in multi-PHD or XML files
report_bases.pl	-	Creates a HTML file reporting on masked, trimmed and good bases for each sequence and the respective averages for a pipeline run
report_filtering.pl	-	Produces a HTML report of the filtering performed on the sequences
report_graphic_complete.pl	-	Generates a detailed graphic report of the quality assignment, vector/primer masking and trimming in multiple HTML files
report_graphic_simple.pl	-	Generates a graphic report of the quality assignment, vector/primer masking and trimming in a single HTML file
snoop_filtered.pl	-	Produces a FASTA, XML or PHD file with either the valid sequences or the sequences invalidated by specified filters.
trimming.pl	-	Trims sequences based on quality and masking
upload_fasta.pl	-	Uploads sequences from a multi-FASTA file
upload_fasta_STDIN.pl	-	Uploads multiple FASTA formatted sequences from standard inputa
upload_phd_dir.pl	-	Uploads PHD files contained in a directory
upload_phd.pl	-	Uploads multiple PHDs from a single concatenated file
upload_traces_phred.pl	Phred	Uploads trace files using Phred for base-calling and quality assignment
upload_seq_names_db.pl	PostgreSQL	Uploads sequences from the database based on their names. Names can be Perl regular expressions. Only runs on database mode.
upload_sql.pl	PostgreSQL	Uploads sequences from the database based on an SQL query. Query should return sequence identifiers. Only runs on database mode.
upload_traces_phred.pl	Phred	Uploads trace files using Phred for base-calling and quality assignment
upload_xml.pl	-	Uploads sequences from an XML file

^aThis program can be used to feed FASTA output from other UNIX software into a pipeline (e.g. using UNIX pipes).