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

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