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How to align simulated sequencing data

This recipe aligns simulated reads with a short read aligner.

1 result • updated 5.1 years ago by Istvan Albert

This recipe aligns simulated reads with a short read aligner.

For more information see the

Bioinformatics Data Analysis online course.
Biostar Handbook for system setup and other information.

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#
# This recipe simulates sequencing data from an accession number.
#
set -uex

# Accession number for the reference.
ACC=AF086833

# How many reads to generate.
N=10000

# Make the genome directory
mkdir -p refs

# This will be the reference genome.
REF=refs/$ACC.fa

# The resulting alignment file.
BAM=align.bam

# Obtain the reference genome.
efetch -db nuccore -format fasta -id $ACC > $REF

# Index reference genome for BWA.
bwa index $REF 2>> runlog.txt

# Index the reference genome for IGV.
samtools faidx $REF

# Generate the simulated reads.
# The mutations will stored in the mutations.txt file.
wgsim -N $N $REF r1.fq r2.fq > mutations.txt 2>> runlog.txt

# Read pair names that are the result of the simulation
R1=r1.fq
R2=r2.fq

# Align the reads and generate the BAM file.
bwa mem $REF $R1 $R2 2>> runlog.txt | samtools sort > $BAM

# Index the alignment file.
samtools index $BAM

# Generate a flagstat.
samtools flagstat $BAM > flagstat.txt

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[acc]
label = "Genome accession number"
display = "TEXTBOX"
value = "AF086833"
regex = "^\\w{1,20}$"
help = "Must be an NCBI accession number"

[N]
label = "The number of reads"
display = "INTEGER"
value = 10000
range = [ 1, 100000,]
help = "How many simulated read pairs to generate."

[settings]
id = 72
recipe_uid = "recipe-simulate"
uid = "recipe-simulate"
name = "How to align simulated sequencing data"
template = "How_to_align_simulated_sequencing_data_bio-data-analysis_72.sh"
image = "How_to_align_simulated_sequencing_data_bio-data-analysis_72.png"
project_uid = "2a988f7f"
url = "http://localhost8000"
help = "This recipe aligns simulated reads with a short read aligner.\n\nFor more information see the\n\n* [Bioinformatics Data Analysis][link]  online course.\n* [Biostar Handbook][book] for system setup and other information.\n\n[link]: https://www.biostarhandbook.com/edu/course/4/\n[book]: https://www.biostarhandbook.com/"

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