Pack a perl program with their dependencies on Ubuntu !
#Follow steps to create your own executable ./web jit@jit-...aticsonline.com/snippets/view/41440/perl-script-to-reads-and-extract-webpage-contents...aluation of genome assembly software based on long readsBy BioStar 409 days ago...1505 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 $PICARD_HOME/picard.jar CollectIns...1331 days ago
1210 days ago
1209 days ago
Download minikraken database !
(JitMetaENV) ➜ day3 curl -O ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/old/mini...r_distrib minikraken2_v2_8GB_201904_UPDATE/hash.k2d #Check for pe reads #kraken2 --use-names --threads 4 --db minikraken2_v2_8GB_201...1208 days ago
990 days ago
Commandline for paired end reads simulation with BBMap !
.../home/urbe/Tools/bbmap/randomreads.sh ref=mixed.fa out=reads_BBMAP250.fq paired interleave...s/bbmap/current/ align2.RandomReads3 build=1 ref=mixed.fa out=rea...3 [build=1, ref=mixed.fa, out=reads_BBMAP250.fq, paired, interlea...paired=true read length=250 reads=100000 insert size=400-600...984 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Down...ect Extending contigs with reads could be done like this: t...correction or extension. reads=-1 Only process th...r the primary kmer counts. threads=X Spawn X hashing t...ck=t Undo changes to reads that have lower coverage for...970 days ago
Trim the reads in loop using Trimmomatic !
for infile in *_1.fastq.gz do base=$(basename ${infile} _1.fastq.gz) trimmomatic PE ${infile} ${base}_2.fastq.gz \ ${base}_1.trim.fastq.gz ${...949 days ago
922 days ago