Results for "C"
Bio-Scripts
Install grabseqs using conda !
vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1111 days ago
Bash script to check installed bioinformatics program !
allTools=(bwa mummer trimomatic) decFlag=0; for name in ${allTools[@]}; do #echo "enter your package name" # read n...$? -ne 0 ] then echo " $name not installed :: Tr...udo apt-get install $name decFlag=1; else...1103 days ago
- conda install -c bioconda megahit Collecting package metadata (current...envs/ added / updated specs: - megahit The fol...h2e03b76_1 2.9 MB bioconda --------------------...#### | 100% Preparing transaction: done Verifying transact...
1103 days ago
- conda install -c bioconda kat Collecting package metadata (current_repodat...ing environment: done ## Package Plan ## environment...8_11 jellyfish bioconda/linux-64::jellyfish-2.2.1...############# | 100% jemalloc-4.5.0 | 6.2 MB | ###...
1103 days ago
- conda install -c bioconda odgi Collecting package metadata (current...envs/ added / updated specs: - odgi The follow...| py37hfecc14a_1 236.6 MB biocond...lloc-5.2.1-h2531618_5 Proceed ([y]/n)? y Downloadin...
1103 days ago
- conda install -c bioconda seqwish Collecting package metadata (current...itENV added / updated specs: - seqwish The fol...h2e03b76_1 4.6 MB bioconda --------------------...#### | 100% Preparing transaction: done Verifying transact...
1103 days ago
Corona variant calling steps !
...name=$(basename "$my_file" .fasta) echo $basename mkdir -p results/sam results/bam results/bcf results/vcf bwa mem trimme...esults/bam/$basename.aligned.bam bcftools mpileup -O b -o results...ults/ rem mkdir "Variant_Results_of_COVID_gz" rem cp -r results/bc...1101 days ago
- #Long reads bedtools bamtofastq -i input.bam -fq output.fastq #For paired-end reads: samtools sort -n input.bam -o input_sorted.bam # sort reads by identifier-name (-n) bedtools bamtofastq -i input_sorted.bam -fq output_r1.fastq -fq2 output_r2.fastq
1053 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.txt1053 days ago
- ...etaENV) ➜ test_phase_assebly conda install -c bioconda bwise Collecting package metadata (current_repodata.json): done S...4.9 MB The following NEW packages will be INSTALLED:...##### | 100% Preparing transaction: done Verifying transact...
1046 days ago
