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25 results for “CAMI 2 Mouse Gut Toy data set”
MaxBin 2.2.7 genome binning of the CAMI 2 Mouse Gut Toy data set, samples 0-63, gold standard pooled assembly
Genome binning of the gold standard pooled assembly <br><strong>Software: </strong>MaxBin<br><strong>SoftwareVersion: </strong>2.2.7<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://sourceforge.net/projects/maxbin/<br><strong>DockerImage:</strong> cami/maxbin:2.2.7<br><strong>IsBiobox:</strong> No<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandUsed:</strong> run_MaxBin.pl -thread 16 -contig anonymous_gsa_pooled.fasta -out output -reads sample_0/reads/anonymous_reads.fq -reads2 sample_1/reads/anonymous_reads.fq -reads3 sample_2/reads/anonymous_reads.fq -reads4 sample_3/reads/anonymous_reads.fq -reads5 sample_4/reads/anonymous_reads.fq -reads6 sample_5/reads/anonymous_reads.fq -reads7 sample_6/reads/anonymous_reads.fq -reads8 sample_7/reads/anonymous_reads.fq -reads9 sample_8/reads/anonymous_reads.fq -reads10 sample_9/reads/anonymous_reads.fq -reads11 sample_10/reads/anonymous_reads.fq -reads12 sample_11/reads/anonymous_reads.fq -reads13 sample_12/reads/anonymous_reads.fq -reads14 sample_13/reads/anonymous_reads.fq -reads15 sample_14/reads/anonymous_reads.fq -reads16 sample_15/reads/anonymous_reads.fq -reads17 sample_16/reads/anonymous_reads.fq -reads18 sample_17/reads/anonymous_reads.fq -reads19 sample_18/reads/anonymous_reads.fq -reads20 sample_19/reads/anonymous_reads.fq -reads21 sample_20/reads/anonymous_reads.fq -reads22 sample_21/reads/anonymous_reads.fq -reads23 sample_22/reads/anonymous_reads.fq -reads24 sample_23/reads/anonymous_reads.fq -reads25 sample_24/reads/anonymous_reads.fq -reads26 sample_25/reads/anonymous_reads.fq -reads27 sample_26/reads/anonymous_reads.fq -reads28 sample_27/reads/anonymous_reads.fq -reads29 sample_28/reads/anonymous_reads.fq -reads30 sample_29/reads/anonymous_reads.fq -reads31 sample_30/reads/anonymous_reads.fq -reads32 sample_31/reads/anonymous_reads.fq -reads33 sample_32/reads/anonymous_reads.fq -reads34 sample_33/reads/anonymous_reads.fq -reads35 sample_34/reads/anonymous_reads.fq -reads36 sample_35/reads/anonymous_reads.fq -reads37 sample_36/reads/anonymous_reads.fq -reads38 sample_37/reads/anonymous_reads.fq -reads39 sample_38/reads/anonymous_reads.fq -reads40 sample_39/reads/anonymous_reads.fq -reads41 sample_40/reads/anonymous_reads.fq -reads42 sample_41/reads/anonymous_reads.fq -reads43 sample_42/reads/anonymous_reads.fq -reads44 sample_43/reads/anonymous_reads.fq -reads45 sample_44/reads/anonymous_reads.fq -reads46 sample_45/reads/anonymous_reads.fq -reads47 sample_46/reads/anonymous_reads.fq -reads48 sample_47/reads/anonymous_reads.fq -reads49 sample_48/reads/anonymous_reads.fq -reads50 sample_49/reads/anonymous_reads.fq -reads51 sample_50/reads/anonymous_reads.fq -reads52 sample_51/reads/anonymous_reads.fq -reads53 sample_52/reads/anonymous_reads.fq -reads54 sample_53/reads/anonymous_reads.fq -reads55 sample_54/reads/anonymous_reads.fq -reads56 sample_55/reads/anonymous_reads.fq -reads57 sample_56/reads/anonymous_reads.fq -reads58 sample_57/reads/anonymous_reads.fq -reads59 sample_58/reads/anonymous_reads.fq -reads60 sample_59/reads/anonymous_reads.fq -reads61 sample_60/reads/anonymous_reads.fq -reads62 sample_61/reads/anonymous_reads.fq -reads63 sample_62/reads/anonymous_reads.fq -reads64 sample_63/reads/anonymous_reads.fq
MEGAHIT 1.0.3, 1.1.3, 1.2.9 assembly of the CAMI 2 Mouse Gut Toy data set, samples 0-9, short reads
<p>Assembly of the first 10 short read samples with different MEGAHIT versions and parameters<br> <strong>Software: </strong>MEGAHIT<br> <strong>SoftwareVersion: </strong>1.0.3, 1.1.3, 1.2.9<br> <strong>DataURL: </strong> https://data.cami-challenge.org/participate<br> <strong>SoftwareURL:</strong> https://github.com/voutcn/megahit<br> <strong>ShortReadsUsed:</strong> True<br> <strong>LongReadsUsed:</strong> False<br> <strong>CommandUsed:</strong> # install bioconda and run:<br> conda create -n megahit103 megahit=1.0.3<br> conda create -n megahit113 megahit=1.1.3<br> conda create -n megahit129 megahit=1.2.9<br> <br> Sample0=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_0/reads/anonymous_reads.fq.gz<br> Sample1=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_1/reads/anonymous_reads.fq.gz<br> Sample2=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_2/reads/anonymous_reads.fq.gz<br> Sample3=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_3/reads/anonymous_reads.fq.gz<br> Sample4=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_4/reads/anonymous_reads.fq.gz<br> Sample5=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_5/reads/anonymous_reads.fq.gz<br> Sample6=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_6/reads/anonymous_reads.fq.gz<br> Sample7=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_7/reads/anonymous_reads.fq.gz<br> Sample8=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_8/reads/anonymous_reads.fq.gz<br> Sample9=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_9/reads/anonymous_reads.fq.gz<br> <br> conda activate megahit103<br> /usr/bin/time -v megahit -t 48 \<br> --12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \<br> -o megahit103-Sample0-9-sLibs-default<br> <br> conda activate megahit113<br> /usr/bin/time -v megahit -t 48 \<br> --12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \<br> -o megahit113-Sample0-9-sLibs-default<br> <br> /usr/bin/time -v megahit -t 48 --presets meta-sensitive \<br> --12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \<br> -o megahit113-Sample0-9-sLibs-meta-sensitive<br> <br> /usr/bin/time -v megahit -t 48 --presets meta-large \<br> --12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \<br> -o megahit113-Sample0-9-sLibs-meta-large<br> <br> conda activate megahit129<br> /usr/bin/time -v megahit -t 48 \<br> --12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \<br> -o megahit129-Sample0-9-sLibs-default</p>
metaSPAdes 3.13.0 assembly of the CAMI 2 Mouse Gut Toy data set, samples 0-9, short reads
<p>Assembly of the first 10 short read samples<br> <strong>Software: </strong>metaSPAdes<br> <strong>SoftwareVersion: </strong>3.13.0<br> <strong>DataURL: </strong> https://data.cami-challenge.org/participate<br> <strong>SoftwareURL:</strong> https://github.com/ablab/spades<br> <strong>ShortReadsUsed:</strong> True<br> <strong>LongReadsUsed:</strong> False<br> <strong>CommandUsed:</strong> conda create -n spades3130 spades=3.13.0-0<br> <br> Sample0=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_0/reads/anonymous_reads.fq.gz<br> Sample1=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_1/reads/anonymous_reads.fq.gz<br> Sample2=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_2/reads/anonymous_reads.fq.gz<br> Sample3=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_3/reads/anonymous_reads.fq.gz<br> Sample4=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_4/reads/anonymous_reads.fq.gz<br> Sample5=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_5/reads/anonymous_reads.fq.gz<br> Sample6=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_6/reads/anonymous_reads.fq.gz<br> Sample7=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_7/reads/anonymous_reads.fq.gz<br> Sample8=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_8/reads/anonymous_reads.fq.gz<br> Sample9=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_9/reads/anonymous_reads.fq.gz<br> <br> cat $Sample0 $Sample1 $Sample2 $Sample3 $Sample4 $Sample5 $Sample6 $Sample7 $Sample8 $Sample9 > Samples0-9_anonymous_reads.fq.gz<br> <br> conda activate spades3130<br> /usr/bin/time -v metaspades.py --12 Samples0-9_anonymous_reads.fq.gz -o metaSPAdes3130-Sample0-9</p>
Gold standard genome and taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly
<p>Gold standard genome and taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly<br> <strong>DataURL: </strong> https://data.cami-challenge.org/participate</p>
Gold standard taxonomic profile of the CAMI 2 Mouse Gut Toy data set, samples 0-63
<p><strong>DataURL: </strong> https://data.cami-challenge.org/participate</p>
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