1511 days ago
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.bam1286 days ago
1166 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 name dpkg -s $name &> /dev/null i...1048 days ago
Corona variant calling steps !
#!/bin/bash FILE_PATH="data/trimmed_fastq_small/" find "$FILE_PATH" -name "*.fasta" | while IFS= read -r my_file do filename=$(basename "$my_file") basename=...1047 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.txt998 days ago
992 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 m...992 days ago
Python script to read FASTA and FASTQ file !
# !/usr/bin/env python3 # -*- coding: utf-8 -*- from pysam import FastxFile def read_fasta_q_file(fasta_q_file): """Parse FASTA/Q file using `pysam.Fa...979 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 asse...978 days ago