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h2fq
matches
snpedia
tomatoaligns
tomatoraw
23medata.txt
2Dfailures.png
2Dpasses.png
Makefile
README.md
ans1_auto.tex
ans2_7_manual.tex
ans2_8_manual.tex
ans2_auto.tex
ans2_manual.tex
ans3_manual.tex
ans4_manual.tex
ans6_manual.tex
ans7_auto.tex
ans8_manual.tex
ans9_manual.tex
assemble.sh
assemble2.sh
bacGenera.txt
bigpie2.PNG
bigratio.py
chr6.py
complement_re-bwa.py
confusionMatrix.py
confusionMatrix2.py
continent.py
dump5.py
extract_qseq.py
fail2D_fastq.txt
failcum1D.png
failcum2D.png
final.aux
final.log
final.pdf
final.tex
final2.pdf
final2.tex
findsnps.py
gengrouping.txt
genomelen.txt
genrat.py
genuspie2.PNG
genusratio.py
getbests.py
getfasta.py
group4_report1_question1.py
group4_report1_question10.py
group4_report1_question11.py
group4_report1_question2.py
group4_report1_question3.py
group4_report1_question4.py
group4_report1_question5.py
group4_report1_question6.py
group4_report1_question7.py
group4_report1_question8.py
group4_report1_question9.py
group4_report2_question6.py
group4_report2_question7.py
header.tex
indel.py
infopipeline.py
infopipeline_2.py
make_seqs.sh
meatorpara.py
meatvenn.py
minrunner.py
mirunner_2.py
mismatch_count.py
part11hist2-eps-converted-to.pdf
part11hist3-eps-converted-to.pdf
part11hist4-eps-converted-to.pdf
part11hist5-eps-converted-to.pdf
part11scatter0mer-eps-converted-to.pdf
part11scatter1mer-eps-converted-to.pdf
part11scatter2mer-eps-converted-to.pdf
part11scatter3mer-eps-converted-to.pdf
part11scatter4mer-eps-converted-to.pdf
part11scatter5mer-eps-converted-to.pdf
part11scatterbd-eps-converted-to.pdf
part2hist-eps-converted-to.pdf
part2hist.eps
pass2D_fastq.txt
passcum1D.png
passcum2D.png
passdf.txt
passtimes.tsv
pieplotter.py
pullfromdir.py
pulltimes.py
q4hh-eps-converted-to.pdf
q4qh-eps-converted-to.pdf
qver.py
readcigar.py
readxml.py
sam_quals.py
searchmany.py
simventer.py
snpedia.py
snplist
splitfails.py
test.py
tomatoalign.py
ughw1 questions 1 6 7.txt
ughw1 questions 3 4 10.txt
updateonsnp.py
withspec.py
yaniv.py
ystrs.py

README.md

ubiq_genome

This code is for the second hackathon of Ubiquitous Genomics.

To run the first part of the assignment, type

make final2.pdf DIR=/wherever/you/put/the/data/

All code in this repository may be used, modified, and/or redistributed under the terms of the GNU General Public License, version 2.0.