after installing cap3

just take a sequence file and use the following terminal at command prompt

cap3 filename [options]

you can specify constraints and qual

CAP3 takes as input a file of sequence reads in FASTA format. If the names of reads contain a dot (‘.’), CAP3 requres that the names of reads sequenced from the same subclone contain the same substring up to the first dot. CAP3 takes two optional files: a file of quality values in FASTA format and a file of forward-reverse constraints.

The file of quality values must be named “xyz.qual”, and the file of forward-reverse constraints must be named “xyz.con”, where “xyz” is the name of the sequence file.

my work involved

input

cap3 seq

seq is the file consisting of some sequence of data…

output

6 files

seq.cap.ace seq.cap.contigs.links seq.cap.info seq.cap.contigs seq.cap.contigs.qual seq.cap.singlets

seq.cap.ace

AS 1 5

CO Contig1 1422 5 11 U NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGTTTT AGTTTTCCTCTGAAGCAAGCACACCTTCCCTTTCCCGTCTGTCTATCCATCCCTGACCCT GTTGTCTGTCTATCCCTGACCCCGTAGTCTCCTAAGTCGCCCCAGATTTTGTGAACACCC TCTGGAACTAGAATCTAGTGGGCGGATGGACCATTTACTAGACGGAGGTAGAGGTGGGTG GATGCGAACGACAGGGTGCATAGTCAGCCCGGTTTTAAGGGCAGGTCACTTGGTAGGTCA GCAGGCGGGTCAGTGGGCGGGTGCCTGCAGCATTTATGAACTTATTTGGCCCAGCAAACA TTTTGAGTGTCAGGCCGTGCCTACCCAAGGTGAGGGTAAGGAGCAAAATCAGCCCAGCCC AGAGCACTGGGTGGCTACACAGAGCCGACCTCTAATGTGCGCTCCGGGTCGGGATGGCAC TCAGCTCGCCTTTAGGGAGTGATGATCTGGATGCCTGGCTTGGAGGTGACAGAGCCTGCC CTTATGAGACAATTAAGAGACTGACTAAGCACCCGGCAGGAGGCCACGAGAATCCCCATG TGAGAAAGAAGAGCATAAACAGGAAACACATTTAATAATTAAACAAAGATAACTCCCTCG TGTGCGCGCACCGGGCCAGCCCCTATAGAAACATCTGAGGAGTCACTTCCTCCCATGACT CTCGCCCGCCCGGCCGGCTGGAGTCGGCTCCTGGCAAGCTTCAGGCACCTCAGTTGTCCT GAATACACACAGCACCCTTTCCTTACTGAAGCCCCTGAGAGCCTCCAGTTCTCCCTCCTT

BQ 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 1$ 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 2$ 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 2$ 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 2$ 20 20 20 20 20 20 20 5 5 5 20 2

AF R3 U 1 AF R1 U 44 AF R2 U 1 AF R4 C 478 AF R6 C 571 BS 1 248 R2 BS 249 250 R3 BS 251 849 R2 BS 850 850 R3 BS 851 974 R2 BS 975 1155 R4 BS 1156 1157 R6 BS 1158 1159 R4 BS 1160 1168 R6 BS 1169 1242 R4 BS 1243 1422 R6

seq.cap.contigs.qual ———————

Contig1 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20

a clear documentation is present about pace at the link below

http://icb.med.cornell.edu/crt/CAP3/example_usage.xml