Assembly of the first 10 short read samples with different MEGAHIT versions and parameters Software: MEGAHIT SoftwareVersion: 1.0.3, 1.1.3, 1.2.9 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/voutcn/megahit ShortReadsUsed: True LongReadsUsed: False CommandUsed: # install bioconda and run: conda create -n megahit103 megahit=1.0.3 conda create -n megahit113 megahit=1.1.3 conda create -n megahit129 megahit=1.2.9 Sample0=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_0/reads/anonymous_reads.fq.gz Sample1=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_1/reads/anonymous_reads.fq.gz Sample2=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_2/reads/anonymous_reads.fq.gz Sample3=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_3/reads/anonymous_reads.fq.gz Sample4=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_4/reads/anonymous_reads.fq.gz Sample5=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_5/reads/anonymous_reads.fq.gz Sample6=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_6/reads/anonymous_reads.fq.gz Sample7=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_7/reads/anonymous_reads.fq.gz Sample8=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_8/reads/anonymous_reads.fq.gz Sample9=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_9/reads/anonymous_reads.fq.gz conda activate megahit103 /usr/bin/time -v megahit -t 48 \ --12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \ -o megahit103-Sample0-9-sLibs-default conda activate megahit113 /usr/bin/time -v megahit -t 48 \ --12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \ -o megahit113-Sample0-9-sLibs-default /usr/bin/time -v megahit -t 48 --presets meta-sensitive \ --12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \ -o megahit113-Sample0-9-sLibs-meta-sensitive /usr/bin/time -v megahit -t 48 --presets meta-large \ --12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \ -o megahit113-Sample0-9-sLibs-meta-large conda activate megahit129 /usr/bin/time -v megahit -t 48 \ --12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \ -o megahit129-Sample0-9-sLibs-default