Gist ac0e4a9bdb2f03d365c4402d04ecba09

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Gist ac0e4a9bdb2f03d365c4402d04ecba09

✓ Published0🌍 Public

Last edited Feb 8, 2019

Created on Feb 8, 2019

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.

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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.

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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.

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Gist aa8c974207019f98e6d45a49488b2c4b

This visualization shows the process of generating pileup files from sequenced reads for a set of 29 samples. The Bash script iterates through a list of sample identifiers, using the `samtools mpileup` command to produce alignment summaries for each sample against a reference genome. The script relies on the command-line APIs of `samtools` for pileup generation, operating on sorted BAM files. The output from this script would be a text-based pileup format, which is not a graphical visualization but a data-preparation step for subsequent analysis. The code references a reference file and a list of SRR accession numbers, indicating the source is genomic sequencing data.

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Gist 454d4384d1fd704c8d1933b01d2c2af4

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Gist 3d7c2ec8630fd8451ee2b2ed513c2c4a

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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.

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Gist b503b3f905281f7da44c76ba5ed1d8d9

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.

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Gist 143778d0c50388a317ebc30c0ec5de86

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