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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.

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