Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires sorted and indexed BAM files as input. Any read aligner + samtools can be used to obtain such files. Read pairs needs to be align...2136 days ago
Long reads mapper bash script !
#!/bin/bash #only for LONG READS mapping #USAGE: runMapper.sh minimap2 ref.fa reads.fa/fq 48 ont echo -e "This is a bash scrip to map your long reads and make it...2134 days ago
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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 sambamb...1571 days ago
Pack a perl program with their dependencies on Ubuntu !
#Follow steps to create your own executable ./web jit@jit-HP-Pro-3335-MT:~/Downloads/autoConTAMPR/bin$ sudo apt install libpar-packer-perl Reading package lists......1523 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") basena...1057 days ago