Pipelines

2012-paper-diginorm

khmer bits

• sandbox/load-into-hashbits.py
• scripts/load-into-counting.py
• scripts/normalize-by-median.py
• scripts/filter-abund.py
• scripts/count-overlap.py
• scripts/count-median.py

external bits

• bowtie-build
• samtools {faidx,view,sort,index}
• bowtie

internal bits

• calc-r2.py
• make-random-genome.py
• make-random-transcriptome.py
• make-reads.py
• make-biased-reads.py
• read-kmer-rank-dist.py
• find-missing-kmers.py
• mapping-genome-cov-3.py
• compare-map-med.py
• mapping-cov-3.py

2013-khmer-counting

khmer bits

• scripts/abundance-dist-single.py
• scripts/load-into-counting.py
• sandbox/hi-lo-abundance-by-position.py
• scripts/filter-abund.py
• scripts/normalize-by-median.py
• scripts/filter-abund-single.py
• sandbox/strip-and-split-for-assembly.py

internal bits

• khmer-count-kmers.py
• jelly-search.sh
• tallymer-search.sh
• get_random_kmers_1M_C3.py
• simulate_random_reads.py
• fp_assessment.py
• count-singleton-kmers-at-end.py
• extract-filter-abund-rounds.py
• ngs-scripts/blast/calc-blast-cover.py

external bits

• jellyfish
• gt {suffixerator,tallymer}
• dsk
• blast: formatdb, blastall