Name		Name	Last commit message	Last commit date
Latest commit History 587 Commits
APPROX_RAIDER_src/src		APPROX_RAIDER_src/src
BIGFOOT_src		BIGFOOT_src
CompositesHunt		CompositesHunt
RAIDER_exact		RAIDER_exact
RAIDER_prescan/src		RAIDER_prescan/src
RAIDER_src/src		RAIDER_src/src
RAIDER_src_v2/src		RAIDER_src_v2/src
RAIDER_src_v2_age1/src		RAIDER_src_v2_age1/src
RAIDER_src_v2_older		RAIDER_src_v2_older
RAIDER_src_v2_options/src		RAIDER_src_v2_options/src
RAIDER_src_v2_options_multi/src		RAIDER_src_v2_options_multi/src
RAIDER_src_v2_options_new/src		RAIDER_src_v2_options_new/src
RUNTIME2		RUNTIME2
RepeatScout.d		RepeatScout.d
aseed_files		aseed_files
data		data
manuscript		manuscript
nseg.d		nseg.d
phRAIDER.d		phRAIDER.d
pra_code		pra_code
pra_code2		pra_code2
repbase		repbase
seqan		seqan
shells		shells
tools		tools
.gitignore		.gitignore
BSB.pptx		BSB.pptx
Carly.README		Carly.README
ICCABS.poster.doc		ICCABS.poster.doc
MaskRepeatScout.sh		MaskRepeatScout.sh
PRA_results.csv		PRA_results.csv
PRA_results.xls		PRA_results.xls
RAIDER_current		RAIDER_current
RAIDER_eval.py		RAIDER_eval.py
README.RepeatScout		README.RepeatScout
README.md		README.md
RepeatScout		RepeatScout
RepeatScout.sh		RepeatScout.sh
RptSct.stats.txt		RptSct.stats.txt
RunRepeatScout.sh		RunRepeatScout.sh
SEEDS15.stats.txt		SEEDS15.stats.txt
SchaefferDefense.tmp.pptx		SchaefferDefense.tmp.pptx
all.stats2.txt		all.stats2.txt
analysis.R		analysis.R
analysis2.R		analysis2.R
analysis3.R		analysis3.R
auto_resubmit_rev.job		auto_resubmit_rev.job
auto_resubmit_rev_R2_sf.job		auto_resubmit_rev_R2_sf.job
auto_resubmit_rev_sf.job		auto_resubmit_rev_sf.job
best.stats.txt		best.stats.txt
best.txt		best.txt
best1.txt		best1.txt
best_seeds_2015.06.05.txt		best_seeds_2015.06.05.txt
bigfoot		bigfoot
biopython-1.64.tar.gz		biopython-1.64.tar.gz
blast_consensus.py		blast_consensus.py
build_lmer_table		build_lmer_table
checkpoint_jobs.py		checkpoint_jobs.py
chromosome_simulator.py		chromosome_simulator.py
chromosome_simulator2.py		chromosome_simulator2.py
chromosome_simulator3.py		chromosome_simulator3.py
cleanup.sh		cleanup.sh
cmd.sh		cmd.sh
collect_runtimes.py		collect_runtimes.py
collect_stats.py		collect_stats.py
consensus_seq.py		consensus_seq.py
coverageBLAST.py		coverageBLAST.py
create_database.py		create_database.py
create_database2.py		create_database2.py
create_pra.py		create_pra.py
doCombinedAnalysis.R		doCombinedAnalysis.R
doSortedAnalysis.R		doSortedAnalysis.R
filter-stage-1.prl		filter-stage-1.prl
filter-stage-2.prl		filter-stage-2.prl
hg.rpt_list.txt		hg.rpt_list.txt
interval_list.py		interval_list.py
locations.py		locations.py
markov_gen.py		markov_gen.py
muscle		muscle
nseg		nseg
out.6.2.txt		out.6.2.txt
pals		pals
parse_pra_output.py		parse_pra_output.py
perform_stats.py		perform_stats.py
piler2		piler2
raider2_poster.pptx		raider2_poster.pptx
raider2_poster2.pptx		raider2_poster2.pptx
random_template.py		random_template.py
redhawk.py		redhawk.py
reformat_seed_stats.py		reformat_seed_stats.py
results.xlsx		results.xlsx
rev_sf.sh		rev_sf.sh
rev_sf_pra.sh		rev_sf_pra.sh
rpt_list.txt		rpt_list.txt
rt1.fa		rt1.fa
run_all.sh		run_all.sh
run_chr.py		run_chr.py
run_piler.py		run_piler.py
run_repeatmasker.py		run_repeatmasker.py
runtime.txt		runtime.txt

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RAIDER_eval

This repository contains verious developmental versions of the RAIDER tool for de novo sequence identification, as well as a set of python scripts used for autmated testing of RAIDER on a PBS cluster. Code includes:

RAIDER_src: Sorce code for original RAIDER prototype.
RAIDER_prescan: Source cod for a low-memory version of RAIDER.
RAIDER_srv_v2: Adaptation of RAIDER to spaced seed searches.
RAIDER_eval.py: Script for automated testing of RAIDER and other de novo search tools.

figuernd/RAIDER_eval

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