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
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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
