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#SBATCH -J jobName

#SBATCH -J spades
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#SBATCH -n 1

#SBATCH -n 4

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#SBATCH -N 1

#SBATCH -N 4

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#SBATCH -t 12:00:00

#SBATCH -t 104:0030:00

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##SBATCH --mail-user=ADD

#SBATCH --mail-user=<YourEmailAddress>

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##SBATCH --mail-type=all

#SBATCH --mail-type=all

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conda activate GVA2021

conda activate GVA-SPAdes

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export LAUNCHER_JOB_FILE=commands

export LAUNCHER_JOB_FILE=spades_commands

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Code Block
languagebash
titleExample grep commands
# Count the total number of contigs:
grep -c "^>" single_end/contigs.fasta

# Determine the length of the 5 largest contigs:
grep "^>" single_end/contigs.fasta | head -n 5

# Determine the length of the 20 smallest contigs:
grep "^>" single_end/contigs.fasta | tail -n 20

# Determine the length of the 100th through 110th contigs:
grep "^>" single_end/contigs.fasta | head -n 110 | tail -n 10

If Since you ran multiple different combinations of reads for the simulated data how did the insert size effect the number of contigs? the length of the largest contigs? Why might larger insert sizes not help things very much?

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