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.bam1275 days ago
1155 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 if [ $? -ne 0...1038 days ago
Corona variant calling steps !
#!/bin/bash FILE_PATH="data/trimmed_fastq_small/" find "$FILE_PATH" -name "*.fasta" | while IFS= read -r my_file do filename=$(basename "$my_file") basename=$(basename "...1037 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.txt988 days ago
982 days ago
Commandline for paired end reads simulation with BBMap !
...✗ /home/urbe/Tools/bbmap/randomreads.sh ref=mixed.fa out=reads_BBMAP250.fq paired interleav...ols/bbmap/current/ align2.RandomReads3 build=1 ref=mixed.fa out=re...ds3 [build=1, ref=mixed.fa, out=reads_BBMAP250.fq, paired, interle...0, len=(0-0) genome=1 PERFECT_READ_RATIO=0.0 ADD_ERRORS_FROM_QU...982 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.FastxFile`....968 days ago
Tadpole is 250x faster than SPADes assembler !
...ect Extending contigs with reads could be done like this:...outd= Write discarded reads, if using junk-removal flags...r the primary kmer counts. threads=X Spawn X hashing...meo=t (markerrorreadsonly) Only mark bad bases in...968 days ago
Inreractive SCP / File transfer !
...s entered value to variable with name desthost read -p "Destination Server Name :...s entered value to variable with name destpath read -p "Destination Path : " dest...s entered value to variable with name filename read -p "Path to source directory...942 days ago