+ mkdir -p db
+ ACC=AF086833
+ REF=db/AF086833.fa
+ READ1=pair1.fq
+ READ2=pair2.fq
+ efetch -db=nuccore -format=fasta -id=AF086833
+ bwa index db/AF086833.fa
+ samtools faidx db/AF086833.fa
+ cp db/AF086833.fa GENOME.fa
+ run_experiment align1.bam
+ BAM=align1.bam
+ wgsim -e 0 -r 0 -R 0 -X 0 -N 2500 GENOME.fa pair1.fq pair2.fq
+ samtools sort
+ bwa mem db/AF086833.fa pair1.fq pair2.fq
+ samtools index align1.bam
+ cat db/AF086833.fa
+ seqret --filter -sbegin 1 -send 2000
+ cat db/AF086833.fa
+ seqret --filter -sbegin 3000
+ cat part1 part2
+ union -filter
+ run_experiment align2.bam
+ BAM=align2.bam
+ wgsim -e 0 -r 0 -R 0 -X 0 -N 2500 GENOME.fa pair1.fq pair2.fq
+ bwa mem db/AF086833.fa pair1.fq pair2.fq
+ samtools sort
+ samtools index align2.bam
+ cat db/AF086833.fa
+ seqret --filter -sbegin 1 -send 2000
+ cat part1 part1 db/AF086833.fa
+ union -filter
+ run_experiment align3.bam
+ BAM=align3.bam
+ wgsim -e 0 -r 0 -R 0 -X 0 -N 2500 GENOME.fa pair1.fq pair2.fq
+ bwa mem db/AF086833.fa pair1.fq pair2.fq
+ samtools sort
+ samtools index align3.bam
+ cat db/AF086833.fa
+ seqret --filter -send 5000
+ cat db/AF086833.fa
+ seqret --filter -sbegin 5000
+ cat part2 part1
+ union -filter
+ run_experiment align4.bam
+ BAM=align4.bam
+ wgsim -e 0 -r 0 -R 0 -X 0 -N 2500 GENOME.fa pair1.fq pair2.fq
+ bwa mem db/AF086833.fa pair1.fq pair2.fq
+ samtools sort
+ samtools index align4.bam
+ cat db/AF086833.fa
+ seqret --filter -sbegin 1 -send 1000
+ cat db/AF086833.fa
+ seqret --filter -sbegin 1000 -send 2000 -sreverse1
+ cat db/AF086833.fa
+ seqret --filter -sbegin 2000
+ cat part1 part2 part3
+ union -filter
+ run_experiment align5.bam
+ BAM=align5.bam
+ wgsim -e 0 -r 0 -R 0 -X 0 -N 2500 GENOME.fa pair1.fq pair2.fq
+ bwa mem db/AF086833.fa pair1.fq pair2.fq
+ samtools sort
+ samtools index align5.bam
+ cat db/AF086833.fa
+ msbar -filter -count 10 -point 1 -block 1 -minimum 10 -maximum 500
+ run_experiment align6.bam
+ BAM=align6.bam
+ wgsim -e 0 -r 0 -R 0 -X 0 -N 2500 GENOME.fa pair1.fq pair2.fq
+ bwa mem db/AF086833.fa pair1.fq pair2.fq
+ samtools sort
+ samtools index align6.bam
+ rm -f part1 part2 part3