ads1-notebooks

Copies of notebooks used in the practical sessions for Algorithms for DNA Sequencing

Algorithms-for-DNA-sequencing

Name		Name	Last commit message	Last commit date
Latest commit History 1 Commit
.gitignore		.gitignore
1.01_StringBasics.ipynb		1.01_StringBasics.ipynb
1.02_ManipulatingDNAStrings.ipynb		1.02_ManipulatingDNAStrings.ipynb
1.03_ParsingRefGenome.ipynb		1.03_ParsingRefGenome.ipynb
1.04_WorkingWithSequencingReads.ipynb		1.04_WorkingWithSequencingReads.ipynb
1.05_AnalyzingReadsByPosition.ipynb		1.05_AnalyzingReadsByPosition.ipynb
1.06_NaiveExactMatching-MatchingArtificialReads.ipynb		1.06_NaiveExactMatching-MatchingArtificialReads.ipynb
1.07_NaiveExactMatching-MatchingRealReads.ipynb		1.07_NaiveExactMatching-MatchingRealReads.ipynb
2.01_BoyerMoore.ipynb		2.01_BoyerMoore.ipynb
2.02_SubstringIndex.ipynb		2.02_SubstringIndex.ipynb
2.03_ApproximateMatching.ipynb		2.03_ApproximateMatching.ipynb
3.01_EditDistanceDP.ipynb		3.01_EditDistanceDP.ipynb
3.02_GlobalAlignment.ipynb		3.02_GlobalAlignment.ipynb
3.03_FindingOverlaps.ipynb		3.03_FindingOverlaps.ipynb
3.04_FindingAllOverlaps.ipynb		3.04_FindingAllOverlaps.ipynb
4.01_ShortestCommonSuperstring.ipynb		4.01_ShortestCommonSuperstring.ipynb
4.02_GreedySCS.ipynb		4.02_GreedySCS.ipynb
4.03_DeBruijn.ipynb		4.03_DeBruijn.ipynb
ERR266411_1.for_asm.fastq		ERR266411_1.for_asm.fastq
README.md		README.md
SRR835775_1.first1000.fastq		SRR835775_1.first1000.fastq
ads1_week4_reads.fq		ads1_week4_reads.fq
bm_preproc.py		bm_preproc.py
bm_preproc.pyc		bm_preproc.pyc
chr1.GRCh38.excerpt.fasta		chr1.GRCh38.excerpt.fasta
homework-1.ipynb		homework-1.ipynb
homework-2.ipynb		homework-2.ipynb
homework-3.ipynb		homework-3.ipynb
homework-4.ipynb		homework-4.ipynb
lambda_virus.fa		lambda_virus.fa
phix.fa		phix.fa

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Algorithms-for-DNA-sequencing

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