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Table 1 Command and parameters used for evaluating EST assembly programs

From: iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences

Program

Command and parameters

iAssembler

iAssembler.pl -i input_est -h 40 -e 30 -p 97 -d -o output ("-e 10" for Arabidopsis)

CAP3

cap3 input_est -o 40 -y 30 -p 97 -f 6 -s 251 ("-y 10" for Arabidopsis)

TGICL

tgicl input_est -l 40 -v 30 -p 97 ("-v 10" for Arabidopsis)

MIRA (olive)

mira -project = project -fasta = input_est -job = denovo, est, normal,454 -notraceinfo -GE:not = 1 454_SETTINGS -LR:wqf = no -AS:epoq = no:mrl = 30 COMMON_SETTINGS -AS:nop = 4 -SK:not = 1:pr = 97 -CL:pec = no 454_SETTINGS -AL:mo = 40:mrs = 97

MIRA (tomato and Arabidopsis)

mira -project = project -fasta = input_est -job = denovo, est, normal, sanger -notraceinfo -GE:not = 1 SANGER_SETTINGS -LR:wqf = no -AS:epoq = no:mrl = 30 COMMON_SETTINGS -AS:nop = 4 -SK:not = 1:pr = 97 -CL:pec = no SANGER_SETTINGS -AL:mo = 40:mrs = 97

Phrap

phrap input_est -ace

Newbler

runAssembly -cdna -urt -notrim -ml 40 -mi 97 -o output input_est