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CISA:
python ${PATH_TO}/CISA1.3/Merge.py Merge.config
python ${PATH_TO}/CISA1.3/CISA.py CISA.config
CISA commands need 2 configuration files as inputs.
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Merge.config (sample)
count=$N #integer, number of input assemblies
assm1=$Assembly1,tool1=$index1
assm2=$Assembly2,tool2=$index2
⋮
assmN=$AssemblyN,toolN=$indexN
min_length=100
Master_file=Merged.ctg.fa
GAP=11
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CISA.config (sample)
genome=$(genome_size) #integer, estimated genome size
infile=${PATH_TO}/Merged.ctg.fa
outfile=${PATH_TO}/CISA.ctg.fa
R2_Gap=0.95
CISA=${PATH_TO}/CISA1.3
nucmer=${PATH_TO}/nucmer
makeblastdb=${PATH_TO}/makeblastdb
blastn=${PATH_TO}/blastn
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GAA:
perl ${PATH_TO}/gaa/gaa.pl -s 100 -p 90 -t $targedAssembly -q $queryAssembly
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GAM_NGS:
To run GAM_NGS, we used their pipeline script provided within the tool's directory at
gam-ngs-1.1b/example/gam-ngs_pipeline.sh. We changed the value of --min-block-size 10 to the default value --min-block-size 50.
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GARM:
perl ${PATH_TO}/GARM_v0.7.3/GARM.pl -m 200 -t 50 -l 200 -g GARM.config -o merged
Where the configuration file contains path to input assemblies and unique their indices,
GARM.config (sample).
$Assembly1_Contigs $index1 #tab separated
$Assembly2_Scaffolds $index2 #tab separated
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Metassembler:
python ${PATH_TO}/Metassembler1.2/bin/metassemble.py --conf Metassemble.config --outd ${PATH_TO}/output_Directory
A configuration file is needed.
Metassemble.config (sample).
[global]
# Mate-pair mapping parameters:
bowtie2_threads=2
bowtie2_read1=${PATH_TO/Reads/shortjump_1.fastq
bowtie2_read2=${PATH_TO/Reads/shortjump_2.fastq
##Staphylococcus_aureus, Rhodobacter_sphaeroides##
bowtie2_minins=3300
bowtie2_maxins=3700
##HG_ch14##
# bowtie2_minins=35295
# bowtie2_maxins=35318
##Bombus_impatiens##
# bowtie2_minins=7500
# bowtie2_maxins=8500
genomeLength=$(genome_size)
# CE-stat computation parameters:
##Staphylococcus_aureus, Rhodobacter_sphaeroides##
mateAn_A=3300
mateAn_B=3700
##HG_ch14##
# mateAn_A=35295
# mateAn_B=35318
##Bombus_impatiens##
# mateAn_A=7500
# mateAn_B=8500
# Whole Genome Alignment parameters:
asseMerge_c=20
asseMerge_l=60
asseMerge_a=60
[1]
fasta=$Assembly1
ID=$index1
[2]
fasta=$Assembly2
ID=$index2
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Mix:
python ${PATH_TO}/MIX-master/bin/Mix.py -a alignments.coords -c contigs.fa -o ${output_dir}
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Zorro:
perl ${PATH_TO}/Zorro2.2/zorro.pl -o 40 -i 94 -g 15 -1 $Assembly1 -2 $Assembly2 -r $reads