GitHub - ThibauldMichel/Targeted_enrichment: Scripts and outline of pipeline to generate robust consensus sequence from targeted captured reads

The file "Hyb_baits_pipeline" provides an outline of how the scripts in this folder were used to generate the data in Nicholls et al., (2015) Frontiers in Plant Biology - Technical Advances Section.

Name		Name	Last commit message	Last commit date
Latest commit History 4 Commits
Concat_nexus.py		Concat_nexus.py
Differential_Inga_picking.py		Differential_Inga_picking.py
Hyb_Baits_pipeline		Hyb_Baits_pipeline
README.md		README.md
Ref.fna		Ref.fna
Switch_multifastas.py		Switch_multifastas.py
bam_me.sh		bam_me.sh
ck_empties.sh		ck_empties.sh
ck_remove.sh		ck_remove.sh
clean_vcf.sh		clean_vcf.sh
commandQ		commandQ
get_vcf_stats.sh		get_vcf_stats.sh
more_tidying.sh		more_tidying.sh
pick_bowtie_parameters.sh		pick_bowtie_parameters.sh
raw_to_fasta.sh		raw_to_fasta.sh
tidy_mafft.sh		tidy_mafft.sh
vcfutils_fasta.pl		vcfutils_fasta.pl

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