Gamete binning

Here we introduce the pipeline for gamete binning, a method based on single-cell sequencing of gamete genomes to achieve chromosome-level and haplotype-resolved genome assembly of a heterozygous species. This is to support the analysis in Campoy_and_Sun_et_al_2020.

Pre-requisite

Note 1: zlib.h is required by some tools (for the purpose of zipping files), please install accordingly.

Note 2: a few publicly available tools are needed,

• bcftools
• blast
• bowtie2
• Canu v1.7
• cellranger-dna
• findGSE
• Flye 2.6-g6f887ae
• jellyfish 2.2.10
• KMC
• purge_haplotigs
• pbalign
• pilon
• samtools
• SHOREmap
• ...

Installation of self-developed tools

Please check INSTALL.

Pipeline of assembly

Please check Pipeline.md