Assembly with Newbler

Files: 454Reads_Brocamacho3_.RL1.sff G0JGIQD01.RL1.sff GY3XZ9M01.RL1.sff GYO778V02.RL1.sff

Extract Reads from Sff

/data/process/Broca/Genoma/Ensamblajes/Ensamble4SffMacho/AssemblyMacho/assembly# /opt/scripts/sff_extract.pl -c —min_left_clip=4 ../sff/*.sff -o TotalReadsMacho

Extract Singletons Ids from Assembly

grep ‘Singleton’ 454ReadStatus.txt | sed ‘s/Singleton//’ > IdsSingletons

cdbfasta TotalReadsMacho.fasta

cdbyank TotalReadsMacho.fasta.cidx < IdsSingletons > Singletons.fasta

cat 454AllContigs.fna Singletons.fasta > GENOMAMACHO.fasta

Masking Male Genome

cp GENOMAMACHO.fasta /data/process/Broca/PipeLineGenomaTotalMacho/

/opt/RepeatModeler/BuildDatabase -name GENOMABROCAMACHO_RMOD.fasta GENOMAMACHO.fasta

/opt/RepeatModeler/RepeatModeler -database GENOMABROCAMACHO_RMOD.fasta > run.out