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mr-c edited this page Aug 26, 2013
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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
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
3rd party
- trimmomatic
- libgtextutils
- fastx
- trinity
- bowtie
- RSEM package: rsem-{prepare-reference,calculate-expression}
- blast/formatdb
khmer bits
- scripts/normalize-by-median.py
- filter-abund.py
- scripts/do-partition.py
custom bits
- eel-pond/rename-with-partitions.py
- eel-pond/make-uni-best-hits.py
- eel-pond/make-reciprocal-best-hits.py
- eel-pond/make-namedb.py
- screed.fadbm (source?)
- eel-pond/annotate-seqs.py
https://github.com/ged-lab/khmer-protocols/blob/master/metagenomics/
third-party
- Trimmomatic
- libgtextutils
- fastx
- gunzip
- velvet
- IDBA
- bowtie
khmer bits
- scripts/normalize-by-median.py
- scripts/filter-abund.py
- scripts/extract-paired-reads.py
- sandbox/readstats.py
- scripts/do-partition.py
- scripts/extract-partitions.py
- sandbox/sweep-reads3.py
- sandbox/assemstats3.py
- sandbox/extract-long-sequences.py
- sandbox/make-coverage.py
https://github.com/ged-lab/khmer/blob/master/examples/stamps/do.sh
khmer bits
- scripts/load-into-counting.py
- scripts/abundance-dist.py
- scripts/normalize-by-median.py
- scripts/do-partition.py
- sandbox/error-correct-pass2.py
- scripts/extract-partitions.py
- scripts/filter-abund.py