genomes (reference) in projects: dports

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Searched refs:genomes (Results 1 – 25 of 391) sorted by relevance

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/dports/biology/graphlan/nsegata-graphlan-66ec7cfce81e/examples/DisappearingMicrobiome/
H A D	run.sh	6 for l in `cat genomes.all.txt \| grep g__Prevotella \| cut -f 1 \| sed -n '0~4p'` ; do echo $l"\tring… 7 for l in `cat genomes.all.txt \| grep g__Xylanibacter \| cut -f 1` ; do echo $l"\tring_width\t2\t8\n"… 9 for l in `cat genomes.all.txt \| grep g__Butyrivibrio \| cut -f 1` ; do echo $l"\tring_width\t2\t8\n"… 18 for l in `cat genomes.all.txt \| grep g__Eubacterium \| cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$… 19 for l in `cat genomes.all.txt \| grep g__Dialister \| cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"… 27 for l in `cat genomes.all.txt \| grep g__Bulleidia \| cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"… 28 for l in `cat genomes.all.txt \| grep g__Gemella \| cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\t… 34 for l in `cat genomes.all.txt \| grep g__Slackia \| cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\t… 35 for l in `cat genomes.all.txt \| grep g__Gemella \| cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\t… 46 for l in `cat genomes.all.txt \| grep g__Dorea \| cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tri… [all …]
/dports/biology/bedtools/bedtools2-2.30.0/test/bamtobed/
H A D	numeric_tag.sam	4 …b4a9304cb5d48026a85128 UR:/uufs/chpc.utah.edu/common/home/u6000771/bcbio/genomes/Hsapiens/g1k_v37_… 5 …0400dec1098a9255ac712e UR:/uufs/chpc.utah.edu/common/home/u6000771/bcbio/genomes/Hsapiens/g1k_v37_… 6 …cc2fadebc929bb925902e5 UR:/uufs/chpc.utah.edu/common/home/u6000771/bcbio/genomes/Hsapiens/g1k_v37_… 7 …97542ad87d2765d28a19a1 UR:/uufs/chpc.utah.edu/common/home/u6000771/bcbio/genomes/Hsapiens/g1k_v37_… 8 …ffd264d728f32784845cd7 UR:/uufs/chpc.utah.edu/common/home/u6000771/bcbio/genomes/Hsapiens/g1k_v37_… 9 …d92a729ee764823acbbc6b UR:/uufs/chpc.utah.edu/common/home/u6000771/bcbio/genomes/Hsapiens/g1k_v37_… 10 …d6aaad97dbe4777c29375e UR:/uufs/chpc.utah.edu/common/home/u6000771/bcbio/genomes/Hsapiens/g1k_v37_… 11 …9e410c6651697bded59aec UR:/uufs/chpc.utah.edu/common/home/u6000771/bcbio/genomes/Hsapiens/g1k_v37_… 12 …5e0a400f01055d9f393768 UR:/uufs/chpc.utah.edu/common/home/u6000771/bcbio/genomes/Hsapiens/g1k_v37_… 13 …e84c26d552359af1ea2e1d UR:/uufs/chpc.utah.edu/common/home/u6000771/bcbio/genomes/Hsapiens/g1k_v37_… [all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/
H A D	collect-read-counts-NA12878-expected.tsv	2 @SQ SN:1 LN:249250621 AS:NCBI37 M5:1b22b98cdeb4a9304cb5d48026a85128 UR:ftp://ftp.1000genomes.ebi.ac… 3 @SQ SN:2 LN:243199373 AS:NCBI37 M5:a0d9851da00400dec1098a9255ac712e UR:ftp://ftp.1000genomes.ebi.ac… 4 @SQ SN:3 LN:198022430 AS:NCBI37 M5:fdfd811849cc2fadebc929bb925902e5 UR:ftp://ftp.1000genomes.ebi.ac… 5 @SQ SN:4 LN:191154276 AS:NCBI37 M5:23dccd106897542ad87d2765d28a19a1 UR:ftp://ftp.1000genomes.ebi.ac… 6 @SQ SN:5 LN:180915260 AS:NCBI37 M5:0740173db9ffd264d728f32784845cd7 UR:ftp://ftp.1000genomes.ebi.ac… 7 @SQ SN:6 LN:171115067 AS:NCBI37 M5:1d3a93a248d92a729ee764823acbbc6b UR:ftp://ftp.1000genomes.ebi.ac… 8 @SQ SN:7 LN:159138663 AS:NCBI37 M5:618366e953d6aaad97dbe4777c29375e UR:ftp://ftp.1000genomes.ebi.ac… 9 @SQ SN:8 LN:146364022 AS:NCBI37 M5:96f514a9929e410c6651697bded59aec UR:ftp://ftp.1000genomes.ebi.ac… 10 @SQ SN:9 LN:141213431 AS:NCBI37 M5:3e273117f15e0a400f01055d9f393768 UR:ftp://ftp.1000genomes.ebi.ac… 11 @SQ SN:10 LN:135534747 AS:NCBI37 M5:988c28e000e84c26d552359af1ea2e1d UR:ftp://ftp.1000genomes.ebi.a… [all …]
/dports/biology/fasta3/fasta-36.3.8/conf/
H A D	fast_libs_e.www	`7 Human/Refseq proteins$0H${SLIB2}/genomes/hum_refseq.lseg 8 Mouse/Refseq proteins$0M${SLIB2}/genomes/mus_refseq.lseg 9 Rat/Refseq proteins$0R${SLIB2}/genomes/rat_refseq.lseg 10 Drosophila/RefSeq proteins$0F${SLIB2}/genomes/d_melanogaster.lseg 11 C. elegans/RefSeq proteins$0W${SLIB2}/genomes/c_elegans.lseg 12 Arabidopsis/RefSeq proteins$0L${SLIB2}/genomes/a_thaliana.lseg 13 Yeast (S. cerevisiae)${SLIB2}/genomes/s_cerevisiae.lseg 14 E. coli proteins$0E${SLIB2}/genomes/ecoli_k12.lseg`
H A D	fast_new	`8 Yeast proteins$0Y/slib0/genomes/yeast_nr.pep 10 E. coli proteome$0E/slib0/genomes/ecoli.npep 11 H. influenzae proteome$0I/slib0/genomes/hinf.npep 12 H. pylori proteome$0L/slib0/genomes/hpyl.npep 14 M. pneumococcus proteome$0M/slib0/genomes/mpneu.npep 15 M. jannaschii proteome$0J/slib0/genomes/mjan.npep 16 Synechosystis proteome$0C/slib0/genomes/synecho.npep 33 E. coli genome$1D/slib0/genomes/ecoli.gbk 1`
H A D	fastlibs	`12 Yeast proteins$0Y/slib0/genomes/yeast_nr.pep 14 E. coli proteome$0E/slib0/genomes/ecoli.npep 15 H. influenzae proteome$0I/slib0/genomes/hinf.npep 16 H. pylori proteome$0L/slib0/genomes/hpyl.npep 18 M. pneumococcus proteome$0M/slib0/genomes/mpneu.npep 19 M. jannaschii proteome$0J/slib0/genomes/mjan.npep 20 Synechosystis proteome$0C/slib0/genomes/synecho.npep 37 E. coli genome$1D/slib0/genomes/ecoli.gbk 1`
/dports/biology/bowtie2/bowtie2-2.4.4/scripts/test/
H A D	btdata.py	`34 self.genomes = dict() 35 self.genomes['human'] = dict() 36 hm = self.genomes['human'] 45 self.genomes['mouse'] = dict() 46 ms = self.genomes['mouse'] 69 for genome,gdata in list(self.genomes.items()): 85 g = self.genomes[genome] 121 g = self.genomes[genome] 161 fasta_file = os.path.join(gn_path,self.genomes[g]['ref_name'])`
/dports/biology/bowtie/bowtie-1.3.1/scripts/test/
H A D	btdata.py	`34 self.genomes = dict() 35 self.genomes['human'] = dict() 36 hm = self.genomes['human'] 45 self.genomes['mouse'] = dict() 46 ms = self.genomes['mouse'] 69 for genome,gdata in list(self.genomes.items()): 85 g = self.genomes[genome] 121 g = self.genomes[genome] 161 fasta_file = os.path.join(gn_path,self.genomes[g]['ref_name'])`
/dports/biology/py-biopython/biopython-1.79/Doc/examples/
H A D	ACT_example.py	`35 genomes = [ variable 42 assert len(genomes) >= 2 and len(genomes) == len(comparisons) + 1 47 for f, format in genomes: 63 q = genomes[i + 1][0] # query file 64 s = genomes[i][0] # subject file 113 for f, format in genomes:`
/dports/biology/bedtools/bedtools2-2.30.0/test/shuffle/
H A D	test-shuffle.sh	`34 -g ../../genomes/human.hg19.genome \| head > obs 65 -g ../../genomes/human.hg19.genome \| head -20 > obs 95 -g ../../genomes/human.hg19.genome \| head -20 > obs 106 -g ../../genomes/human.hg19.genome \ 128 -g ../../genomes/human.hg19.genome \`
/dports/biology/abyss/abyss-2.3.1/
H A D	CITATION.md	`4 ABySS 2.0: Resource-efficient assembly of large genomes using a Bloom filter. 17 title={ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter}, 34 Jackman, Shaun D., et al. "ABySS 2.0: resource-efficient assembly of large genomes using a Bloom fi… 38 … ... & Birol, I. (2017). ABySS 2.0: resource-efficient assembly of large genomes using a Bloom fil… 42 …d, Golnaz Jahesh et al. "ABySS 2.0: resource-efficient assembly of large genomes using a Bloom fil…`
/dports/biology/prodigal/Prodigal-2.6.3-7-ga78ed3f/
H A D	README.md	`3 Fast, reliable protein-coding gene prediction for prokaryotic genomes. 34 …* Handles draft genomes and metagenomes: Prodigal runs smoothly on finished genomes, draft gen…`
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/micro_razers/
H A D	outputFormat.h	155 TGenomes &genomes, in getErrorDistribution() argument 168 genome = infix(genomes[(it).gseqNo], (it).gBegin, (it).gEnd); in getErrorDistribution() 187 TGenomes &genomes, in getErrorDistribution() argument 212 assignSource(row(align, 1), infix(genomes[(it).gseqNo], (it).gBegin, (it).gEnd)); in getErrorDistribution() 325 TGenomeSet genomes; in dumpMatches() local 327 if (!loadGenomes(genomes, genomeFileNameList)) { in dumpMatches() 338 for (unsigned l = length(genomes); l > 9; l = l / 10) in dumpMatches() 456 assignSource(row(align, 1), infix(genomes[(it).gseqNo], (it).gBegin, (*it).gEnd)); in dumpMatches() 575 unique = getErrorDistribution(posError, matches, reads, genomes, options); in dumpMatches() 578 … unique = getErrorDistribution(posError, insertions, deletions, matches, reads, genomes, options); in dumpMatches()
/dports/biology/bbmap/bbmap/pipelines/fetch/
H A D	fetchMito.sh	`3 wget -q -O - ftp://ftp.ncbi.nih.gov/genomes/refseq/mitochondrion/genomic.gbff.gz > mito.genomic.gb… 4 wget -q -O - ftp://ftp.ncbi.nih.gov/genomes/refseq/mitochondrion/genomic.fna.gz > mito.genomic.fna…`
H A D	fetchPlastid.sh	`3 wget -q -O - ftp://ftp.ncbi.nih.gov/genomes/refseq/plastid/genomic.gbff.gz > plastid.genomic.gbff.… 4 wget -q -O - ftp://ftp.ncbi.nih.gov/genomes/refseq/plastid/genomic.fna.gz > plastid.genomic.fna.gz`
H A D	fetchPlasmid.sh	`3 wget -q -O - ftp://ftp.ncbi.nih.gov/genomes/refseq/plasmid/genomic.gbff.gz > plasmid.genomic.gbff.… 4 wget -q -O - ftp://ftp.ncbi.nih.gov/genomes/refseq/plasmid/genomic.fna.gz > plasmid.genomic.fna.gz`
H A D	fetchProkByGenus.sh	`1 time fetchproks.sh ftp://ftp.ncbi.nih.gov:21/genomes/refseq/archaea archaea.sh 1>fetchA.o 2>&1 2 time fetchproks.sh ftp://ftp.ncbi.nih.gov:21/genomes/refseq/bacteria bacteria.sh 1>fetchB.o 2>&1`
/dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/docs/
H A D	run-mummer1.README	`26 O. White, and S.L. Salzberg. Alignment of whole genomes. 37 512Mb to align most pairs of bacterial genomes, and 1Gb or more may be 42 the steps of aligning two genomes. The script takes these arguments: 46 The two genomes must DNA sequences in FASTA format. Multi-FASTA 54 of the two genomes by the program. In between the MUMs are gaps, 70 Columns 1 and 2 are the positions of a MUM in genomes 1 and 2. The`
/dports/biology/bowtie2/bowtie2-2.4.4/scripts/
H A D	make_m_musculus_ncbi37.sh	`13 M_MUS_FTP=ftp://ftp.ncbi.nih.gov/genomes/M_musculus/Assembled_chromosomes 14 M_MUS_MT_FTP=ftp://ftp.ncbi.nih.gov/genomes/M_musculus/CHR_MT`
/dports/biology/bowtie/bowtie-1.3.1/scripts/
H A D	make_m_musculus_ncbi37.sh	`13 M_MUS_FTP=ftp://ftp.ncbi.nih.gov/genomes/M_musculus/Assembled_chromosomes 14 M_MUS_MT_FTP=ftp://ftp.ncbi.nih.gov/genomes/M_musculus/CHR_MT`
/dports/biology/hisat2/hisat2-2.2.1/evaluation/
H A D	build_indexes.py	`14 genomes = ["22_20-21M", "22", "genome"] 15 for genome in genomes:`
/dports/biology/bedtools/bedtools2-2.30.0/test/slop/
H A D	test-slop.sh	`160 echo -e "chr1\t16778271\t16778571"\| $BT slop -l 200 -r 200 -i - -g ../../genomes/human.hg19.genome … 170 echo -e "chr1\t16778272\t16778572"\| $BT slop -l 200 -r 200 -i - -g ../../genomes/human.hg19.genome … 178 echo -e "chr1\t160\t170\nchr1\t100\t200"\| $BT slop -b 0.1 -pct -i - -g ../../genomes/human.hg19.gen…`
/dports/biology/canu/canu-2.2/src/meryl/documentation/source/
H A D	quick-start.rst	22 …curl -LRO ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/522/225/GCA_014522225.1_ASM1452222v1/GCA_… 23 …curl -LRO ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/165/095/GCA_002165095.2_ASM216509v2/GCA_0… 24 …curl -LRO ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/071/835/GCA_905071835.1_MSB1_4I/GCA_90507… 60 genomes into one database, all in one command. 88 from all three genomes are combined into one database, summing the counts for 151 EC931. Histograms from the other two genomes show either no high copy repeat 154 kmers and see where they are on the genomes.
/dports/lang/rust/rustc-1.58.1-src/src/test/ui/did_you_mean/
H A D	issue-48492-tuple-destructure-missing-parens.rs	`82 let genomes = Vec::new(); in main() localVariable 84 let women, men: (Vec<Genome>, Vec<Genome>) = genomes.iter().cloned() in main()`
/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/models/
H A D	protein.bf	`17 …ecialist empirical model of protein evolution for metazoan mitochondrial genomes from Le, Dang, an… 18 …ialist empirical model of protein evolution for vertebrate mitochondrial genomes from Le, Dang, an… 19 …list empirical model of protein evolution for invertebrate mitochondrial genomes from Le, Dang, an… 20 …cialist empirical model of protein evolution for green plant chloroplast genomes from from Cox an…`

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