Name		Name	Last commit message	Last commit date
Latest commit History 217 Commits
src		src
.gitignore		.gitignore
2023-02-13--count-read-distribution.py		2023-02-13--count-read-distribution.py
2023-02-13--count-read-distribution.sh		2023-02-13--count-read-distribution.sh
2023-02-13--count-read-prefixes.py		2023-02-13--count-read-prefixes.py
2023-02-13--count-read-prefixes.sh		2023-02-13--count-read-prefixes.sh
Cargo.lock		Cargo.lock
Cargo.toml		Cargo.toml
LICENSE		LICENSE
Makefile		Makefile
README.md		README.md
align-reads-to-contigs.sh		align-reads-to-contigs.sh
assemble-spike-contigs.sh		assemble-spike-contigs.sh
assemble.py		assemble.py
assemble2.py		assemble2.py
baseline-max-growth-single.sh		baseline-max-growth-single.sh
baseline-max-growth.sh		baseline-max-growth.sh
bucket-counts.py		bucket-counts.py
ca.KX342792.1.fasta		ca.KX342792.1.fasta
cat-n-socal.sh		cat-n-socal.sh
cgmmv.NC_001801.1.fasta		cgmmv.NC_001801.1.fasta
chart-daily-reads-for-threshold.py		chart-daily-reads-for-threshold.py
close-shm.c		close-shm.c
collate-kmer-counts.py		collate-kmer-counts.py
combine-tbrv-alignment-points.py		combine-tbrv-alignment-points.py
combine-wtp-summaries.py		combine-wtp-summaries.py
compute-correlation.py		compute-correlation.py
compute-correlation.sh		compute-correlation.sh
compute-mean-and-variance-seq.sh		compute-mean-and-variance-seq.sh
compute-mean-and-variance-single.sh		compute-mean-and-variance-single.sh
compute-mean-and-variance.py		compute-mean-and-variance.py
compute-mean-and-variance.sh		compute-mean-and-variance.sh
copy-results-to-s3.sh		copy-results-to-s3.sh
count-consistent-timeseries.sh		count-consistent-timeseries.sh
count-dups.sh		count-dups.sh
count-kmer-eqs.c		count-kmer-eqs.c
count-kmer-eqs.py		count-kmer-eqs.py
count-kmers-simulated-day.sh		count-kmers-simulated-day.sh
count-kmers-simulated-days.sh		count-kmers-simulated-days.sh
count-quality.py		count-quality.py
count-reads-matching-contigs.py		count-reads-matching-contigs.py
count-reads-tbrv.sh		count-reads-tbrv.sh
count-spike-pcr-duplicates.py		count-spike-pcr-duplicates.py
count-wtp.sh		count-wtp.sh
cross-val.py		cross-val.py
dedup-poisson.py		dedup-poisson.py
determine-barcodes.sh		determine-barcodes.sh
determine-insert-lengths.sh		determine-insert-lengths.sh
determine-match-accuracy.py		determine-match-accuracy.py
determine-read-contig-starts.py		determine-read-contig-starts.py
display-all-reads.sh		display-all-reads.sh
download-and-c.sh		download-and-c.sh
download-and-extract.sh		download-and-extract.sh
download-and-rust.sh		download-and-rust.sh
dump-all.sh		dump-all.sh
eval-buckets-sm.py		eval-buckets-sm.py
eval-buckets.py		eval-buckets.py
eval-wtp.sh		eval-wtp.sh
evaluate-socal-hashing.sh		evaluate-socal-hashing.sh
extract-kmer-counts-wtp.sh		extract-kmer-counts-wtp.sh
extract-kmer-counts.py		extract-kmer-counts.py
extract-kmer-counts.sh		extract-kmer-counts.sh
extract-kmers.c		extract-kmers.c
extract-overlapping-reads.py		extract-overlapping-reads.py
extract-reads-matching-seq.py		extract-reads-matching-seq.py
extract-reads-matching-seq.sh		extract-reads-matching-seq.sh
extract-reads-matching-spike-kmers.py		extract-reads-matching-spike-kmers.py
extract-spike-reads.sh		extract-spike-reads.sh
fasta-to-ecs.c		fasta-to-ecs.c
fetch-ec-counts.sh		fetch-ec-counts.sh
fetch-kmer-counts.py		fetch-kmer-counts.py
find-aligning-reads.py		find-aligning-reads.py
find-aligning-reads.sh		find-aligning-reads.sh
find-all-spikes.sh		find-all-spikes.sh
find-best-seeds.py		find-best-seeds.py
find-best-seeds.sh		find-best-seeds.sh
find-best-timeseries.py		find-best-timeseries.py
find-best-timeseries.sh		find-best-timeseries.sh
find-kmer-matching-reads.py		find-kmer-matching-reads.py
find-massive-dups.sh		find-massive-dups.sh
find-min-hcu-poisson-p-values.sh		find-min-hcu-poisson-p-values.sh
find-reads-single.sh		find-reads-single.sh
find-reads.sh		find-reads.sh
find-spikes.py		find-spikes.py
find-subsetted-kmers.sh		find-subsetted-kmers.sh
flat_hash_map.hpp		flat_hash_map.hpp
generate-unenriched-count-cdfs.py		generate-unenriched-count-cdfs.py
group-spikes.py		group-spikes.py
growth-rate-comparison.py		growth-rate-comparison.py
hash-count-rothman.cpp		hash-count-rothman.cpp
hash-count-single.cpp		hash-count-single.cpp
hash-count-union.cpp		hash-count-union.cpp
hash-count-variable.cpp		hash-count-variable.cpp
hash-count.cpp		hash-count.cpp
hc-HTP-full-summary		hc-HTP-full-summary
hiv.fasta		hiv.fasta
iterative-assembler-clean-up.py		iterative-assembler-clean-up.py
iterative-assembler.c		iterative-assembler.c
iterative-assembler.py		iterative-assembler.py
iterative-assembler.sh		iterative-assembler.sh

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K-mer Exponential Growth Detection

Reference-free detection of exponentially growing sequences in untargeted genetic sequencing.

Current code is quick drafts for testing feasibility of various methods.

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