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,

Installation of self-developed tools

Please check INSTALL.

Pipeline of assembly

Please check Pipeline.md

Name		Name	Last commit message	Last commit date
Latest commit History 73 Commits
R_scripts_aux		R_scripts_aux
dependency_src_gzstream		dependency_src_gzstream
dev_bin		dev_bin
file_aux		file_aux
src_10x_barcode_trimmer		src_10x_barcode_trimmer
src_JoinMap_contig_phasing_checker		src_JoinMap_contig_phasing_checker
src_as10xbamFqer		src_as10xbamFqer
src_asCellseparator		src_asCellseparator
src_asScaffolder		src_asScaffolder
src_break_contig_3688		src_break_contig_3688
src_cell_wise_potential_co_or_noise_checker		src_cell_wise_potential_co_or_noise_checker
src_del_regional_s1_markers_finder		src_del_regional_s1_markers_finder
src_del_regional_s2_depth_finder		src_del_regional_s2_depth_finder
src_del_regional_s3_genotypes_finder		src_del_regional_s3_genotypes_finder
src_long_read_separator		src_long_read_separator
src_s6_pollen_bed_with_JoinMap_contig_phasing_flipper		src_s6_pollen_bed_with_JoinMap_contig_phasing_flipper
src_scaffolder		src_scaffolder
INSTALL		INSTALL
LICENSE		LICENSE
Pipeline.md		Pipeline.md
README.md		README.md
asPollinator_1.0		asPollinator_1.0
asPollinator_1.0.cpp		asPollinator_1.0.cpp
makefile		makefile
split_string.cpp		split_string.cpp
split_string.h		split_string.h

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dineshpalli/GameteBinning

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Gamete binning

Pre-requisite

Installation of self-developed tools

Pipeline of assembly

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