Bioinformatics Data Analysis

Run Parameters
Parameters used during the run:
  • Genome accession number: AF086833
  • The number of reads: 10000
File List
Files created by the recipe run:
Output Messages
Messages printed to the standard output stream:

    
Other Messages
Messages printed to the standard error stream:
+ ACC=AF086833
+ COUNT=10000
+ BAM=align.bam
+ REF=refs/AF086833.fa
+ mkdir -p refs
+ efetch -db=nuccore -format=fasta -id=AF086833
+ bwa index refs/AF086833.fa
+ samtools faidx refs/AF086833.fa
+ REAL=real.fa
+ cat refs/AF086833.fa
+ seqret --filter -sbegin 1 -send 2000
+ cat refs/AF086833.fa
+ seqret --filter -sbegin 3000
+ cat part1 part2
+ union -filter
+ R1=r1.fq
+ R2=r2.fq
+ wgsim -e 0 -r 0 -R 0 -N 10000 real.fa r1.fq r2.fq
+ bwa mem refs/AF086833.fa r1.fq r2.fq
+ samtools sort
+ samtools index align.bam
+ samtools flagstat align.bam

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