Print the screenshot of read coverage remotely !
#Chrom_2:9700000-9760000 ASCIIGenome -ni --fasta A_vaga.NDPD.fasta -r Chrom_2:9700000-9760000 -x "save >> test.pdf" A_vaga.NDPD.fasta.out.sam.bam.sorted.bam1307 days ago
1187 days ago
Bash script to check installed bioinformatics program !
allTools=(bwa mummer trimomatic) decFlag=0; for name in ${allTools[@]}; do #echo "enter your package name" # read...1069 days ago
Corona variant calling steps !
#!/bin/bash FILE_PATH="data/trimmed_fastq_small/" find "$FILE_PATH" -name "*.fasta" | while IFS= read...1068 days ago
Commandline to Extract a list of specific read IDs from a bam file
#Save all the IDs in IDs.txt file #Run it on BAM file samtools view file.bam | fgrep -w -f IDs.txt1019 days ago
1013 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 interleav...s/bbmap/current/ align2.RandomReads3 build=1 ref=mixed.fa out=re...3 [build=1, ref=mixed.fa, out=reads_BBMAP250.fq, paired, interle...len=(0-0) genome=1 PERFECT_READ_...1013 days ago
Python script to read FASTA and FASTQ file !
# !/usr/bin/env python3 # -*- coding: utf-8 -*- from pysam import FastxFile def read_...1000 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Down...r the primary kmer counts. threads=X Spawn X hashing...meo=t (markerrorreadsonly) Only mark bad bases in...xtended. Pairs are removed only if both read...s depth. Pairs are removed if either read fa...999 days ago
Inreractive SCP / File transfer !
#!/bin/bash #next line prints hearer of script echo "Interactive Script...value to variable with name desthost read -p "Destination Server Name :...value to variable with name destpath read -p "Destination Path : " dest...value to variable with name filename read...973 days ago