Results for "Java."
Bio-Scripts
➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ ./Trinity --seqType fq --max_memory 250G --left /media/urbe/MyPassport/rnaseq_boris/AIG_AAAOSW_8_1_C1CBGACXX.IND11_norib...2141 days ago
- ...2.1/gatk-package-4.0.2.1-local.jar --help OpenJDK 64-Bit Server VM warning: Insufficient space for shared memory file: 13132 Try using the -Djava.io.tmpdir= option to select an...
2089 days ago
Installing pb-assembly on Linux !
[jnarayan@hmem00 ~]$ module avail -------------------------------------------------------- /usr/share/Modules/modulefiles -----------------------------------------...2048 days ago
CollectGcBiasMetrics.jar will generate a GC bias plot for each contig
samtools index aln-pe.mapped.sorted.bam for i in $(samtools view -H aln-pe.mapped.sorted.bam | awk -F"\t" '/@SQ/{gsub("^SN:","",$2);print $2}' ); do samtools view...2017 days ago
- jit@jit-HP-Pro-3335-MT:~$ java -version openjdk version "11.0.6" 2020-01-14 OpenJDK Runtime Environment (build 11.0.6+10-post-Ubuntu-1ubuntu118.04.1) OpenJDK 64-Bit...
1553 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 $P...1350 days ago
Commandline for paired end reads simulation with BBMap !
(JitMetaENV) ➜ mixedSample git:(main) ✗ /home/urbe/Tools/bbmap/randomreads.sh ref=mixed.fa out=reads_BBMAP250.fq paired interleaved reads=100k length=250 mininsert=40...1003 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/Vir$ tadpole.sh Written by Brian Bushnell Last modified July 16, 2018 Description: Uses kmer counts to a...990 days ago
- # Make sure that Java v8+ is installed: java -version # Install Nextflow curl -fsSL get.nextflow.io | bash # Add Nextflow binary to your PATH: mv nextflow ~/bin/ # OR system-wide installation: # sudo mv nextflow /usr/local/bin
976 days ago
Install Varscan on Ubuntu / Linux !
#Varscan is a java program designed to call variants in sequencing data. It was developed at the Genome Institute at Washington University and is hosted on github. To...837 days ago
