BOL: Nanopolis: polish a genome assembly

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Rahul Nayak
Nanopolis: polish a genome assembly

Nanopolis: polish a genome assembly

By Rahul Nayak 2310 days ago Comments (1)

Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below).

Quickstart

http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html

Algorithms

http://simpsonlab.github.io/2017/06/30/nanopolish-v0.7.0/

Comments

Rahul Nayak 2299 days ago

# Index the draft genome
bwa index draft.fa

# Align the basecalled reads to the draft sequence
bwa mem -x ont2d -t 8 draft.fa reads.fa | samtools sort -o reads.sorted.bam -T reads.tmp -
samtools index reads.sorted.bam

python nanopolish_makerange.py draft.fa | parallel --results nanopolish.results -P 8 \
    nanopolish variants --consensus -o polished.{1}.vcf -w {1} -r reads.fa -b reads.sorted.bam -g draft.fa -t 4 --min-candidate-frequency 0.1


nanopolish vcf2fasta -g draft.fa polished.*.vcf > polished_genome.fa

BOL

Rahul Nayak

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Nanopolis: polish a genome assembly

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