Recipe View

This recipe is a Makefile that executes the bwa and bbmap aligners.

0 results • updated 4 months ago by Istvan Albert • needs authorization

This recipe is a Makefile that executes the bwa and bbmap aligners.

Usage:

make genome

Download reads:

make reads

Run bwa:

make bwa

Run bbmap:

make bbmap

Or run everything at once:

 make genome reads bwa

Copy recipe

You need write access to the project to edit.

# How to set up your new environment.
#
# conda create --clone bioinfo --name bbmap
# conda activate bbmap
# mamba install bbmap

# Reference genome accession number.
ACC=CM000684

# The SRR number for the sequencing data.
SRR=SRR1039508

# Alignment files for both methods.
BAM_BWA=${SRR}-${ACC}-bwa.bam

BAM_BBMAP=${SRR}-${ACC}-bbmap.bam

# Readcount
N=10000

# The name for the read pairs.
R1=reads/${SRR}_1.fastq
R2=reads/${SRR}_2.fastq

# The reference genome stored locally.
REF=refs/${ACC}.fa

genome:
	mkdir -p refs
	bio fetch -format fasta ${ACC} > ${REF}
	samtools faidx ${REF}
	time bwa index ${REF}
	time bbmap.sh ref=${REF}

data:
	# Obtain the FASTQ sequences for the SRR number.
	mkdir -p reads
	fastq-dump -F -X ${N} --split-files ${SRR} -O reads

bwa:
	# Run the bwa aligner. Creates a SAM file.
	bwa mem -t 4 ${REF} ${R1} ${R2} | samtools sort > ${BAM_BWA}
	samtools index ${BAM_BWA}
	samtools flagstat ${BAM_BWA}

bbmap:
	# Run the bwa aligner. Creates a SAM file.
	bbmap.sh in1=${R1} in2=${R2} ref=${REF} out=out.sam trd=t
	cat out.sam | samtools sort > ${BAM_BBMAP}
	samtools index ${BAM_BBMAP}
	samtools flagstat ${BAM_BBMAP}

bbmap2:
	# Run the bwa aligner with "different" parameters.
	bbmap.sh in1=${R1} in2=${R2} ref=${REF} out=out.sam k=8 maxindel=200 minratio=0.1 trd=t
	cat out.sam | samtools sort > ${BAM_BBMAP}
	samtools index ${BAM_BBMAP}
	samtools flagstat ${BAM_BBMAP}

coverage:
	bedtools bamtobed -i ${BAM_BWA} > test.bed

You need write access to the original recipe to edit.

Click the buttons on the right to create new fields.

Add text field Add float field Add data field Add checkbox Add dropdown Add upload field Add integer field Add radio button

Name

Recipe display name

Identifier

Unique identifier for the recipe.

Image :

Optional image for the recipe ( 500px Maximum ).

Rank:

Used to order recipes (optional).

Insert Image

From the web

From your computer

Cancel

Back

Evaluate the BBMAP aligner

Insert Image