Powerful oneliners for quick data processing in bioinformatics

There are many command-line tools and utilities that can be useful in bioinformatics for quick data processing, analysis, and manipulation. Some of these oneliner tools include:

• awk: A versatile text processing tool that can be used to filter, reformat, and transform data.

  awk '{print $1}' input.txt
  

• sed: A stream editor for filtering and transforming text.

  sed 's/A/T/g' input.txt > output.txt
  

• grep: A tool to search for patterns in text files.

  grep "ATG" input.fasta

• sort: Sorts lines in a text file.

  sort input.txt > sorted_input.txt

• uniq: Removes duplicate lines from a sorted file or displays the number of occurrences of each line.

  uniq -c input.txt > unique_counts.txt

• wc: Counts lines, words, and characters in a file.

  wc -l input.txt

• cut: Removes sections from each line of a file.

  cut -f1,3 input.txt > output.txt

• paste: Joins corresponding lines of multiple files.

  paste file1.txt file2.txt > combined.txt

• tr: Translates or deletes characters.

  tr 'atcg' 'TAGC' < input.txt > output.txt

• curl: Transfers data from or to a server.

  curl -O "https://example.com/file.fasta"

• bioawk: An extension of awk with built-in functions for biological data.

  bioawk -c fastx '{print $name, length($seq)}' input.fasta

• seqkit: A cross-platform toolkit for FASTA/Q file manipulation.

  seqkit stat input.fasta

• Samtools is a widely-used suite of tools for manipulating and analyzing high-throughput sequencing (HTS) data in the SAM, BAM, and CRAM formats. Here are some examples of how you can use Samtools for various tasks:

• Convert SAM to BAM format: To convert a SAM (Sequence Alignment/Map) file to a compressed binary BAM (Binary Alignment/Map) file, you can use the samtools view command with the -bS option: samtools view -bS input.sam > output.bam

• Sort a BAM file: To sort a BAM file by genomic coordinates, you can use the samtools sort command: samtools sort input.bam -o sorted_output.bam

• Index a sorted BAM file: To create an index for a sorted BAM file, which allows you to quickly access alignments overlapping particular genomic regions, you can use the samtools index command:

  samtools index sorted_output.bam

• Generate an alignment statistics report: To create a summary report of alignment statistics, such as the number of mapped and unmapped reads, you can use the samtools flagstat command:

  samtools flagstat input.bam > report.txt

• Extract reads aligned to a specific region: To extract reads aligned to a specific genomic region, you can use the samtools view command with the -h option and the region of interest:

  samtools view -h input.bam chr1:10000-20000 > region_output.bam

• Filter alignments: To filter alignments based on specific criteria, such as minimum mapping quality, you can use the samtools view command with the -q option:

  samtools view -q 20 input.bam > filtered_output.bam

• Generate a pileup: To create a pileup file from a BAM file, which displays the sequencing depth at each position of the reference genome, you can use the samtools mpileup command:

  samtools mpileup -f reference.fasta input.bam > output.pileup

• Bcftools is a set of utilities for variant calling and manipulating VCF (Variant Call Format) and BCF (Binary Call Format) files. Here are some examples of how you can use Bcftools for various tasks:

• Call variants: To call variants from a BAM or CRAM file using the consensus caller, you can use the bcftools mpileup command followed by bcftools call:

  bcftools mpileup -Ou -f reference.fasta input.bam | bcftools call -mv -Ov -o output.vcf

• Filter variants: To filter variants based on specific criteria, such as quality or depth, you can use the bcftools filter command:

  bcftools filter -i 'QUAL > 20 && DP > 10' input.vcf -o filtered_output.vcf

• View VCF/BCF file: To view the contents of a VCF or BCF file, you can use the bcftools view command:

  bcftools view input.vcf

• Sort a VCF file: To sort a VCF file by genomic coordinates, you can use the bcftools sort command:

  bcftools sort input.vcf -o sorted_output.vcf

• Index a VCF file: To create an index for a VCF or BCF file, which allows you to quickly access variants overlapping specific genomic regions, you can use the bcftools index command:

  bcftools index sorted_output.vcf

• Concatenate multiple VCF files: To concatenate multiple VCF files, ensuring that they have the same sample columns in the same order, you can use the bcftools concat command:

  bcftools concat input1.vcf input2.vcf -o combined_output.vcf

• Generate consensus sequences: To create consensus sequences by applying VCF variants to a reference genome, you can use the bcftools consensus command:

  bcftools consensus -f reference.fasta input.vcf.gz > consensus.fasta

• Normalize indels: To normalize indels in a VCF file (left-align and trim indels), you can use the bcftools norm command:

  bcftools norm -f reference.fasta input.vcf -o normalized_output.vcf

• Bedtools is a powerful suite of tools for working with genomic intervals in various file formats, such as BED, GFF/GTF, and VCF. Here are some examples of how you can use Bedtools for various tasks:

• Intersect intervals: To find overlapping intervals between two files, you can use the bedtools intersect command:

  bedtools intersect -a input1.bed -b input2.bed > output.bed

• Merge intervals: To merge overlapping or adjacent intervals in a single file, you can use the bedtools merge command:

  bedtools merge -i input.bed > output.bed

• Subtract intervals: To subtract intervals in one file from another, you can use the bedtools subtract command:

  bedtools subtract -a input1.bed -b input2.bed > output.bed

• Get genomic sequences: To extract sequences from a reference genome corresponding to intervals in a BED file, you can use the bedtools getfasta command:

  bedtools getfasta -fi reference.fasta -bed input.bed -fo output.fasta

• Sort intervals: To sort genomic intervals by chromosome and start position, you can use the bedtools sort command:

  bedtools sort -i input.bed > sorted_output.bed

• Calculate coverage: To compute the depth at each position or the depth for each interval in a BED file, you can use the bedtools coverage command:

  bedtools coverage -a input1.bed -b input2.bed > output.bed

• Find closest features: To find the closest feature in another file for each feature in a BED file, you can use the bedtools closest command:

  bedtools closest -a input1.bed -b input2.bed > output.bed

• Compute statistics: To calculate various summary statistics for each feature in a BED file, such as the mean, median, or standard deviation of scores, you can use the bedtools groupby command:

  bedtools groupby -i input.bed -g 1 -c 5 -o mean,median,stdev > output.bed

You can often combine these tools using pipes (|) to create powerful oneliners for complex data processing tasks.

~~END~~

like unlike

点赞本文的读者

还没有人对此文章表态

本文有评论

没有评论

看文章，发评论，不要沉默