2120 days ago
2068 days ago
Installing pb-assembly on Linux !
....4.0 Tcl/8.6.7-GCCcore-6.4.0 Java/1.7.0_21...Theano/0.5.0-goolf-1.4.10-Python-2.7.3 Java/1.8.0_152...2027 days ago
CollectGcBiasMetrics.jar will generate a GC bias plot for each contig
...ped.sorted.bam | awk -F"\t" '/@SQ/{gsub("^SN:","",$2);print $2}' ); do samtools view -b aln-pe.mapped.sorted.bam $i > aln-pe.mapped.sorted.$i.bam; java -Xmx2g -jar $(which CollectGc...1997 days ago
1532 days ago
picard tools command to get some insert statistics
#picard tools to get some insert statistics to see whether our reads seem to be in the correct place #module load picard/2.0.1 java -Xmx16g -XX:PermSize=8g -jar $PICARD_HOME/pica...1330 days ago
Commandline for paired end reads simulation with BBMap !
...e/urbe/Tools/bbmap/randomreads.sh ref=mixed.fa out=reads_BBMAP250.fq paired interleaved reads=100k length=250 mininsert=400 maxinsert=600 gaussian java -ea -Xmx162129m -cp /home/urb...983 days ago
Tadpole is 250x faster than SPADes assembler !
...around the read merge junctions. If it appears that the merge created new errors, undo it. Java Parameters: -Xmx This will be passed to Java to set memory usage, overridi...969 days ago
955 days ago
Install Varscan on Ubuntu / Linux !
#Varscan is a java program designed to call variants in sequencing d...file into our ~/workspace/bin. As with the other java programs which have already b...stalled in this section we can invoke Varscan via java -jar. # Install Varscan c...816 days ago