Protocol Online logo
Top : Forum Archives: : Bioinformatics and Biostatistics

Base calling - Base calling (Mar/11/2008 )


All the sequences done for most of my work is outsourced, and the sequence are not base called, it is usually done by the machine program and then is sent to me, I have found so many base calls errors manually using "Finch TV", I would like to know if there is any free down loadable program that would do the base callings equal or better then manually.

Please let me know of only free softwares, I do know a few are expensive softwares that can do the job.



you could use phred/phrap/consed. it is free, you have to provide some information saying it is not for commercial use and about the base calling you can set the parameters regarding quality to discard all the bases that are wrong. please note: it is done through command line, no graphic interphase as far as i know.

i believe also the vector nti does the job. you have to suscribe to invitrogen for that one and it's for free too if you're not a commercial user.