Gist b503b3f905281f7da44c76ba5ed1d8d9

100%

Gist b503b3f905281f7da44c76ba5ed1d8d9

✓ Published0🌍 Public

Last edited Feb 8, 2019

Created on Feb 8, 2019

This example demonstrates a Bash script that trims raw FASTQ sequencing reads using the `fastq-mcf` tool from the ea-utils package. It shows how to process multiple paired-end files in a batch, reading a list of sample identifiers from `fastq/list_run` and applying a quality cutoff of Q20. The script iterates over each sample, takes the forward read file (`${i}_1.fastq.gz`), and generates a trimmed output file (`${i}_1_trim.fastq`) in the same directory. Adapter sequences are specified in `$TPDIR/misc/adap_illumina.fas`, and the output is written to the project’s fastq folder.

AI-generated description

Similar vizzes

Loading thumbnail…

Gist 9a3defa4596db38a11fc0ec9549b4834

This example demonstrates a preprocessing workflow for raw paired-end Illumina sequencing data. It shows the trimming of low-quality bases and removal of adapter sequences using the `fastq-mcf` tool from the ea-utils suite, followed by quality control reporting with `FastQC`. The script runs `fastq-mcf` with parameters for a minimum quality score of 20, a mean quality threshold, and a 150-base pair read length, producing trimmed FASTQ files. These outputs are then processed by `FastQC` to generate quality assessment reports for both the forward and reverse reads, illustrating a standard bioinformatics pipeline for high-throughput sequence data preparation.

NNpfn

85% match

Loading thumbnail…

Gist d5a955d9a667be4ff4afe7064affbb31

This example demonstrates a bioinformatics mapping workflow for processing sequencing reads. The shell script uses the BWA alignment tool to map trimmed FASTQ files from multiple clones against a reference genome (NC_012967.fas). It first indexes the reference with `bwa index`, then iterates through a list of runs from `fastq/list_run`, performing alignment with `bwa aln` using four threads and converting the results to SAM format with `bwa samse` while adding read-group metadata via the `-r` flag. The script outputs aligned SAM files into the `mapping` directory.

NNpfn

70% match

Loading thumbnail…

Gist e3718d6464d2ba18e5a08233edd0aeb1

This Perl script splits a multi-sequence FASTA file into individual FASTA files, one per sequence. It reads the input file line by line, opens a new output file whenever a header line starting with `>` is encountered, and writes the header and subsequent sequence lines to that file. The code uses the `open`, `close`, and `shift` built-in functions to manage up to 248 output files named `CEG0.fasta` through `CEG247.fasta`. The script demonstrates a simple file-parsing and output-splitting workflow for bioinformatics sequence data.

NNpfn

69% match

Loading thumbnail…

Gist 3d7c2ec8630fd8451ee2b2ed513c2c4a

This example documents the assembly of a microbial genome from paired-end Illumina sequencing data. It shows the command-line workflow that converts raw FASTQ files to FASTA format and then performs a de novo assembly using the IDBA-UD software. The script demonstrates the use of the `fq2fa` utility to merge and convert paired reads, followed by an `idba_ud` assembly run with a single thread. The final assembly output is moved to a dedicated directory for further analysis, illustrating a typical bioinformatics pipeline for genomic sequence reconstruction.

NNpfn

68% match

Loading thumbnail…

Gist 454d4384d1fd704c8d1933b01d2c2af4

This example shows a batch processing workflow for sequencing alignment files, automating the conversion of SAM files into sorted, indexed BAM files. The shell script iterates over a list of run identifiers, using the `samtools view` command to filter out unmapped reads with the `-F 4` flag, then pipes the output to `samtools sort` to create order-preserved BAM output. Each resulting file is indexed with `samtools index` for downstream genomic analysis. The script operates within a directory structure defined by the `$TPRESEQ` environment variable.

NNpfn

66% match

Loading thumbnail…

Gist c994b5a229194ab2c98a8580d48f54ef

This example shows a Perl script that corrects FASTA sequence headers by replacing pipe characters with hyphens, making the files compatible with the CEGMA genome analysis tool. The script reads an input FASTA file and writes the corrected output to a second file. It uses the standard Perl file I/O operations `open`, `close`, and the regex substitution operator to modify only the header lines that begin with `>[A-Z]{3}`. The script also checks for an existing output file to prevent accidental overwriting, and it prints a usage message if the correct number of arguments is not provided.

NNpfn

66% match

Loading thumbnail…

Gist ac0e4a9bdb2f03d365c4402d04ecba09

This example shows a command-line workflow for detecting genetic variants from sequencing reads mapped to a reference genome. It first uses `samtools mpileup` to generate a binary call format (BCF) file, then `bcftools call` to produce a VCF file of variants. A second, independent variant call is made using `freebayes` with a ploidy setting of one, outputting its own VCF. The script processes all sorted BAM files in a mapping directory, using the NC_012967.fas reference, demonstrating two standard variant-calling pipelines for haploid samples.

NNpfn

65% match

Loading thumbnail…

Gist 39d6a8d17d83eb8f17c0926e30809957

This example shows a variant-filtering pipeline for genomic data, using bcftools to process VCF files from two different callers (samtools mpileup and freebayes). The script applies quality and proximity filters, including minimum QUAL scores, distance to indels, and indel cluster thresholds, via the bcftools filter command with options like `-i'%QUAL>10'`, `-g3`, and `-G10`. The output writes filtered VCF files with a LOWQUAL annotation for variants that fail the criteria. The code relies on the bcftools command-line API rather than a visualization library, and the data source is the initial VCF files in the variants directory.

NNpfn

64% match