A tool for generating partial genomes

trace2seq FAQs

Frequently asked questions (and answers)

trace2seq Instructions
trace2seq uses phred to basecall raw chromatograph traces and (if you wish) cross_match
to screen vector and/or E.coli sequence. Therefore you will need to have phred and cross_match installed and in your path. You will be prompted for the directory containing the trace files to be processed. It is highly reccommended that 1) this directory contains only trace files and 2) that you don't run trace2seq from this directory. For an explaination of the phred and cross_match parameters see the relevant documentation - if in doubt, use the defaults. To screen for vector and/or E.coli you will need to know the location of your vector.seq file and/or your ecoli.seq file, again see cross_match documentation for more information. trace2seq will produce a directory containing raw basecalled sequence files in FASTA format (raw_fasta), a directory of processed sequence files in FASTA format (trimmed_fasta) and a directory containing phred output (phred_output).
The 2 numbers in the header of the processed sequence FASTA files, represent the start and end of the high quality part of the sequence, as determined by phred quality scores. The vector_screened and ecoli_vector_screened files contain the raw, FASTA format sequences with vector and/or E.coli masked by X's.
CAUTION: trace2seq is a computer program and therefore the output it produces is only as good as the input it is given!
Queries and compliments to nematode.bioinf@ed.ac.uk - Have fun!