Description

Align 10X data using Longranger and FreeBayes to a genome assembly and polish

Input

Name
Description
Pattern

ch_assemblies

Input assemblies to be polished. Should be a concatenation of all haplotypes.

Structure: [meta, fasta]

ch_illumina_10x_reads

Illumina 10X reads to use for polishing, in FastQ format.

Strucure: [meta, [reads]]

Output

Name
Description
Pattern

polished_assembly

The final polished assemblies

assembly_consensus

The consensus polished assembly output by bcftools/consensus, containing all haplotypes

longranger_bam

BAM file of mapped 10X reads to the combined assembly by Longranger

longranger_bai

BAM index of Longranger BAM

longranger_summary

CSV file describing longranger mapping results

merged_vcf

Merged VCF of variants called by Freebayes across the combined assembly

merged_vcf_tbi

Index for VCF

Components

Command copied!