1229 days ago
1228 days ago
Download minikraken database !
(JitMetaENV) ➜ day3 curl -O ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/old/m...mer_distrib minikraken2_v2_8GB_201904_UPDATE/hash.k2d #Check for pe reads #kraken2 --use-names --threads 4 --db minikraken2_v2_8GB_201...1227 days ago
Perl script to run awk inside perl
#!/usr/local/bin/perl eval 'exec /usr/local/bin/perl -S $0 ${1+"$@"}' if $running_under_some_shell; # this emula...output record separator while () { chomp; # strip record separator @Fld = split...1176 days ago
1009 days ago
Commandline for paired end reads simulation with BBMap !
.../home/urbe/Tools/bbmap/randomreads.sh ref=mixed.fa out=reads_BBMAP250.fq paired interleave...s/bbmap/current/ align2.RandomReads3 build=1 ref=mixed.fa out=rea...3 [build=1, ref=mixed.fa, out=reads_BBMAP250.fq, paired, interlea...paired=true read length=250 reads=100000 insert size=400-600...1003 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~...ect Extending contigs with reads could be done like this: t...correction or extension. reads=-1 Only process th...r the primary kmer counts. threads=X Spawn X hashing t...ck=t Undo changes to reads that have lower coverage for...989 days ago
Trim the reads in loop using Trimmomatic !
for infile in *_1.fastq.gz do base=$(basename ${infile} _1.fastq.gz) trimmomatic PE ${infile} ${base}_2.fastq.gz \ ${base}_1.trim.fastq.gz ${...967 days ago
941 days ago
Bash script to simulate a genome !
# Reference https://github.com/chhylp123/hifiasm/issue...pe0.fasta.gz # make reference for randomreads.sh # randomreads.sh part of BBTools/BBMap http...max 12000bp /genetics/elbers/bbmap-38.86/randomreads.sh build=1 \ ow=t seed=1 \...930 days ago