Bioinformatics Data Analysis

Results generated by running the recipe.

Parameters used during the run:

  • Accession number for the reference genome:KM034562
  • SRA run number:SRR1972739
Output Messages
Messages printed to the standard output stream:

Other Messages
Messages printed to the standard error stream:
+ ACC=KM034562
+ SRR=SRR1972739
+ N=10000
+ REF=refs/KM034562.fa
+ mkdir -p refs
+ efetch -db=nuccore -format=fasta -id=KM034562
+ bwa index refs/KM034562.fa
+ samtools faidx refs/KM034562.fa
+ fastq-dump -X 10000 --split-files SRR1972739
+ R1=SRR1972739_1.fastq
+ R2=SRR1972739_2.fastq
+ bwa mem refs/KM034562.fa SRR1972739_1.fastq SRR1972739_2.fastq
+ cat SRR1972739.sam
+ samtools sort
+ samtools index SRR1972739.bam
+ samtools flagstat SRR1972739.bam

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