View Process Hh 06
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