nanopore~pilon

Pilon is an automated genome assembly improvement and variant detection tool.

input_1:FASTA

input_1/scaffolds.fasta

>contig_1
GGGTATTGAAAACCTATGGTGAAGATTCCATTCCCGCTGTCCATTCCATCCTTTCATCCT
TCCATTTCCTCCTTCCATTCCATTTCCTTCCTTCCTTCATTCCATCCATTCCATTTTCCA
TTCCATTCCTGTCCATCCATCGTCCATTCCTTCCATTCCTTCCATTCCATTTCCTTCTCC
TCCTTTTCCATTCCTCCATTCCATTCCTCCATTCCATCCATTCCATCCATTCCTTCCATC
CTCATTCCTTCCTCCTTCCGTCCATTCCATCCTGTCCATTCCTCCATCCTCCATTCCTTC
CGTCCTTCCTCCATTCCATTCATCTTGTCCGTCCATTCCTCCATTCCTATCCATTCCGTC
CATTCCATTCCATCCATTCCATTCCATCCATTCCTTCCATTCCGTCCATTCCATCCATCC
ATTCCATTCATCTTTCCTCCATTCCATTCCATTCCTTCCTTCCATTTCCATTCCATCCAT
TCCATTCCGTCCATTTCCTTCCATTCCTTCCATTTCCTCCATCCATTTCCATCCATCTCC

input_2:sorted BAM (.bam)

input_2/scaffolds.fasta-DRR015801_1.fastq.gz.bam

Option

-c "8" -m "32" -p ""

Output

pilon.fasta

>contig_1_pilon
GGGTATTGAAAACCTATGGTGAAGATTCCATTCCCGCTGTCCATTCCATCCTTTCATCCTTCCATTTCCTCCTTCCATTC
CATTTCCTTCCTTCCTTCATTCCATCCATTCCATTTTCCATTCCATTCCTGTCCATCCATCGTCCATTCCTTCCATTCCT
TCCATTCCATTTCCTTCTCCTCCTTTTCCATTCCTCCATTCCATTCCTCCATTCCATCCATTCCATCCATTCCTTCCATC
CTCATTCCTTCCTCCTTCCGTCCATTCCATCCTGTCCATTCCTCCATCCTCCATTCCTTCCGTCCTTCCTCCATTCCATT
CATCTTGTCCGTCCATTCCTCCATTCCTATCCATTCCGTCCATTCCATTCCATCCATTCCATTCCATCCATTCCTTCCAT
TCCGTCCATTCCATCCATCCATTCCATTCATCTTTCCTCCATTCCATTCCATTCCTTCCTTCCATTTCCATTCCATCCAT
TCCATTCCGTCCATTTCCTTCCATTCCTTCCATTTCCTCCATCCATTTCCATCCATCTCCATCCATCCATCCATCCATCC
TTCCTTCCATTCCATTCCTTCCATCCTTCCATTCCTTCCTTGTCCATCCATTCCTTCCGTCCATTCCCTTTCCATCCATT
CCATTTCCGTCCATTTCCATCCATTCCTTTCCTTTCCTTCCTCCATTCGTCCATTCCTTCCATTTCCTTCCATTCTTCCA

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