Applied Bioinformatics Course Recipes

Results generated by running the recipe.

Parameters used during the run:

  • Genome accession number: AF086833
  • The number of reads: 100000
Output Messages
Messages printed to the standard output stream:

Other Messages
Messages printed to the standard error stream:
+ ACC=AF086833
+ mkdir -p refs
+ REF=refs/AF086833.fa
+ BAM=align.bam
+ bio fetch -format fasta AF086833
+ bwa index refs/AF086833.fa
+ samtools faidx refs/AF086833.fa
+ R1=read1.fq
+ R2=read2.fq
+ pywgsim -N 10000 refs/AF086833.fa read1.fq read2.fq
+ bwa mem refs/AF086833.fa read1.fq read2.fq
+ samtools sort
+ samtools index align.bam
+ freebayes -C 10 -f refs/AF086833.fa align.bam

Powered by the release 2.3.6