Results for "PA"
Bio-Scripts
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 "$my_file" .fasta)...1102 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
- ...lving environment: done ## Package Plan ## environment...- bwise The following packages will be downloaded:...4.9 MB The following NEW packages will be INSTALLED:...Downloading and Extracting Packages certifi-2021.5.30 |...
1047 days ago
Commandline for paired end reads simulation with BBMap !
...ref=mixed.fa out=reads_BBMAP250.fq paired interleaved reads=100k le...ref=mixed.fa out=reads_BBMAP250.fq paired interleaved reads=100k le...ef=mixed.fa, out=reads_BBMAP250.fq, paired, interleaved, reads=100k,..._QUALITY=true REPLACE_NOREF=false paired=true read length=250 re...1047 days ago
List of string comparison algorithms !
String comparison: Levenshtein Distance Damerau-Levenshtein Distance Jaro Distance Jaro-Winkler Distance Match Rating Approach Comparison Hamming Distance More at https://jellyfish.readthedocs.io/en/latest/comparison.html1039 days ago
- Lenovo-ideapad-320-15ISK:~/Downloads/MyTool...install jellyfish Reading package lists... Done Building...mation... Done The following packages were automatically inst...em. The following additional packages will be installed: l...lecting previously unselected package libjellyfish-2.0-2:amd64...
1038 days ago
Python script to read FASTA and FASTQ file !
...ysam import FastxFile def read_fasta_q_file(fasta_q_file): """Parse FASTA/Q file using `pysam.FastxFile`. Args: fasta_q_file (str): Path to FASTA/Q file. ""...1033 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyTool...Second input file for paired data. extra= Extr...inprob for the prefilter. prepasses=1 Use this many p...enome size estimation. contigpasses=16 Build contigs with...thbad=f (rbb) Only discard pairs if both reads are low-dept...1033 days ago
- # Make sure that Java v8+ is installed: java -version # Install Nextflow curl -fsSL get.nextflow.io | bash # Add Nextflow binary to your PATH: mv nextflow ~/bin/ # OR system-wide installation: # sudo mv nextflow /usr/local/bin
1019 days ago
Run multiple bash command in screen !
#login to screen screen -r 123 #bash.sh srun --partition=compute --nodes=1 --ntasks-per-node=40 --pty bash.sh #Run and check the status in screen contol +A +D1019 days ago
