2126 days ago
Installing Porechop on Ubuntu !
➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Porechop.git Cloning into 'Porechop'... remote: Counting objects: 1579, done. remote: Total 1579 (delta 0), reused 0 (delt...2108 days ago
Bash script to alignment of short reads against reference genome !
bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \ E.coli_K12_MG1655.fa SRR1770413_1.fastq.gz SRR1770413_2.fastq.gz \ | samtools view -b - >SRR1770413.raw.bam sambamba sort SRR1770413....1562 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
#Need to download i-adhore-3.0.01.tar.gz from https://wdiceryfd4rjn74bjhhtz2k5di--bioinformatics-psb-ugent-be.translate.goog/webtools/i-adhore/licensing/ #Follow these steps (wgd...1206 days ago
1166 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=400 maxinsert=600 ga...992 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 assemble contigs, e...979 days ago