WGAC

Scripts used for whole genome analysis comparison (WGAC). See WGAC_HOWTO.pdf for more details.

Name		Name	Last commit message	Last commit date
Latest commit History 264 Commits
JABPerlMod		JABPerlMod
globalViewFakeChromosome		globalViewFakeChromosome
parasight		parasight
pipeline		pipeline
stupid_sun_programs		stupid_sun_programs
trim_ends		trim_ends
wgac_programs		wgac_programs
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
Trim.pl		Trim.pl
WGAC_HOWTO.pdf		WGAC_HOWTO.pdf
align		align
align0		align0
align_fast2_batch4.pl		align_fast2_batch4.pl
align_fast3.pl		align_fast3.pl
align_scorer2.pl		align_scorer2.pl
align_scorer_batch2.pl		align_scorer_batch2.pl
all_wgac.py		all_wgac.py
batch_node_copy.py		batch_node_copy.py
bedBases.sh		bedBases.sh
blast64.sh		blast64.sh
blast_align_by_align_overlap_fix3.pl		blast_align_by_align_overlap_fix3.pl
blast_defractionate3.pl		blast_defractionate3.pl
blast_defuguize_hit_by_hit.pl		blast_defuguize_hit_by_hit.pl
blast_fugu.snake		blast_fugu.snake
blast_hit_by_hit_welder2.pl		blast_hit_by_hit_welder2.pl
blast_lav_break_self_overlap2.pl		blast_lav_break_self_overlap2.pl
blast_lav_break_self_overlap2_for_lastz.pl		blast_lav_break_self_overlap2_for_lastz.pl
blast_lav_hit_by_hit.pl		blast_lav_hit_by_hit.pl
blast_lav_hit_by_hit_for_lastz.pl		blast_lav_hit_by_hit_for_lastz.pl
blast_wgac_matcher.py		blast_wgac_matcher.py
blastall		blastall
blastparser.py		blastparser.py
blastparser42.pl		blastparser42.pl
blowups.pst		blowups.pst
checkIfBlastSucceeded.sh		checkIfBlastSucceeded.sh
checkIfTrimEndsSucceeded.sh		checkIfTrimEndsSucceeded.sh
checkIfWgacAlignSucceeded.sh		checkIfWgacAlignSucceeded.sh
chromosome_blowups.pl		chromosome_blowups.pl
chromosome_blowups.txt		chromosome_blowups.txt
chromosome_blowups_GRCh37.pl		chromosome_blowups_GRCh37.pl
chromosome_blowups_PPY.pl		chromosome_blowups_PPY.pl
chromosome_blowups_Ych.pl		chromosome_blowups_Ych.pl
chromosome_blowups_Ych_mmu.pl		chromosome_blowups_Ych_mmu.pl
chromosome_blowups_Ych_pantro2.pl		chromosome_blowups_Ych_pantro2.pl
chromosome_blowups_bd35.pl		chromosome_blowups_bd35.pl
chromosome_blowups_cow.pl		chromosome_blowups_cow.pl
chromosome_blowups_dm3.pl		chromosome_blowups_dm3.pl
chromosome_blowups_pantro2.pl		chromosome_blowups_pantro2.pl
chromosome_blowups_platypus.pl		chromosome_blowups_platypus.pl
chromosome_blowups_zfinch.pl		chromosome_blowups_zfinch.pl
collectTrim.pl		collectTrim.pl
compute_summary_stats.sh		compute_summary_stats.sh
config.sh		config.sh
coordsMerger_sort.pl		coordsMerger_sort.pl
countBasesACGT		countBasesACGT
countBasesACGT.c		countBasesACGT.c
didEnoughGlobalAlignmentsSucceed.py		didEnoughGlobalAlignmentsSucceed.py
dirBlowupP2p.pl		dirBlowupP2p.pl
dir_cat		dir_cat
examineAlignment.py		examineAlignment.py
fasta_findNs.pl		fasta_findNs.pl
fasta_fractionate		fasta_fractionate
fasta_fuguize.pl		fasta_fuguize.pl
fasta_fuguize_batch.pl		fasta_fuguize_batch.pl
fasta_length		fasta_length
fasta_only_ATCGN.pl		fasta_only_ATCGN.pl
fasta_subseq33.pl		fasta_subseq33.pl
filterByTokenValue.py		filterByTokenValue.py
for_parasight.sh		for_parasight.sh
for_parasight_just_chromosomes.sh		for_parasight_just_chromosomes.sh
formatdb		formatdb
fugumation.pl		fugumation.pl
fugumation_lav1.pl		fugumation_lav1.pl
general_pipe		general_pipe
general_pipe.c		general_pipe.c
general_pipe.py		general_pipe.py
getLenStat4Cull-2K.pl		getLenStat4Cull-2K.pl
getLenStat4Cull.pl		getLenStat4Cull.pl
getSimStat4Cull-05.pl		getSimStat4Cull-05.pl
getSimStat4Cull.pl		getSimStat4Cull.pl
global_align.snake		global_align.snake
global_align_110k.snake		global_align_110k.snake
globalview10k.pst		globalview10k.pst
lastparse.pl		lastparse.pl
lastz_self.snake		lastz_self.snake
loadOOWELD2Mysqltable.pl		loadOOWELD2Mysqltable.pl
loadOOWELD2genomicSuperDupFile.pl		loadOOWELD2genomicSuperDupFile.pl
longer_to_shorter_lines.py		longer_to_shorter_lines.py
longer_to_shorter_lines.sh		longer_to_shorter_lines.sh
makeTrack.pl		makeTrack.pl
make_excel_summary.py		make_excel_summary.py
make_oo.weild10kb.join.all.cull.sh		make_oo.weild10kb.join.all.cull.sh
make_oo.weild10kb.join.all.sh		make_oo.weild10kb.join.all.sh
make_trim_jobs.sh		make_trim_jobs.sh
makefile_wgac		makefile_wgac
maskOutGenFromLowCase.pl		maskOutGenFromLowCase.pl
maskOutGenFromNs.pl		maskOutGenFromNs.pl
mergeHit.pl		mergeHit.pl

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