samtools merge merged.bam *hicup.bam &
samtools sort -n -@ 4 -o merged-sorted.bam merged.bam
samtools view merged-sorted.bam |awk 'BEGIN {FS="\t"; OFS="\t"} {name1=$1; str1=and($2,16); chr1=$3; pos1=$4; mapq1=$5; getline; name2=$1; str2=and($2,16); chr2=$3; pos2=$4; mapq2=$5; if(name1==name2) { if (chr1>chr2){print name1, str2, chr2, pos2,1, str1, chr1, pos1, 0, mapq2, mapq1} else {print name1, str1, chr1, pos1, 0, str2, chr2, pos2 ,1, mapq1, mapq2}}}' | sort -k3,3d -k7,7d > readnamesort.txt &

cat readnamesort.txt |perl -ne 'if ($_ =~ /group1.*group1/){print $_}' >g1-readnamesort.txt &
cat readnamesort.txt |perl -ne 'if ($_ =~ /group2.*group2/){print $_}' >g2-readnamesort.txt &
cat readnamesort.txt |perl -ne 'if ($_ =~ /group3.*group3/){print $_}' >g3-readnamesort.txt &
cat readnamesort.txt |perl -ne 'if ($_ =~ /group4.*group4/){print $_}' >g4-readnamesort.txt &
cat readnamesort.txt |perl -ne 'if ($_ =~ /group5.*group5/){print $_}' >g5-readnamesort.txt &
cat readnamesort.txt |perl -ne 'if ($_ =~ /group6.*group6/){print $_}' >g6-readnamesort.txt &
cat readnamesort.txt |perl -ne 'if ($_ =~ /group7.*group7/){print $_}' >g7-readnamesort.txt &

perl -e 'for($i=1;$i <=7;$i++){system("grep ^group$i groups.agp|tail -1|cut -f 1,3 >group$i.size");}'
perl -e 'for($i=1;$i <=7;$i++){system("grep ^group$i groups.agp >group$i.agp");}'
perl -e 'for($i=1;$i <=7;$i++){system("python agp2assembly.py group$i.agp group$i.assembly");}'
sed -i 's/group//g' g*readnamesort.txt
sed -i 's/group//g' *.size
sed -i 's/group//g' g*.agp
perl -e 'for($i=1;$i <=7;$i++){system("java -jar juicer_tools.jar pre g$i-readnamesort.txt g$i-v1.hic group$i.size")}'

For the purposes of comparing against a known reference, generating a rough MUMmer plot of your assembly may be useful as well. Parameters shown below are to generate a quick and dirty plot, as the default will run for over a week on large legume genomes.

Sample:

nucmer -b 50 -l 500 -p IG72623-v1-vsLcb50l500 /isilon/groups/lentil/Lcu/Lcu.2RBY/pseudo/Lens_culinaris_2.0.fasta groups.asm.fasta

Use Juicebox to run a manual review of each chromosome by loading the .hic in and the contig information in the 'open assembly' option. I am not going to detail the manual correction process here, details can be found in Juicebox documentation. Edits can be saved as a .review.assembly file, which will be used as the input to the next step.

Create new pseudomolecules based on changes made in Juicebox, re-run ALLHiC build and step 6 as necessary until satisfied with the pseudomolecules.

If contigs are broken during the Juicebox phase, the contig fasta file needs to be modified accordingly; a fragmentation script is provided. In addition, the tour files created from the review.assembly files will need to be manually edited for naming and to remove debris.

Sample:

cat group1.review.assembly|perl build-tour-from-review.pl >group1.tour
cat group2.review.assembly|perl build-tour-from-review.pl >group2.tour
cat group3.review.assembly|perl build-tour-from-review.pl >group3.tour
cat group4.review.assembly|perl build-tour-from-review.pl >group4.tour
cat group5.review.assembly|perl build-tour-from-review.pl >group5.tour
cat group6.review.assembly|perl build-tour-from-review.pl >group6.tour
cat group7.review.assembly|perl build-tour-from-review.pl >group7.tour
grep fragment group*.review.assembly >fragments.txt 
cat fragments.txt |perl -plane '$_ =~ s/group.*assembly:>//;$_ =~ s/:::/\t/g;$_ =~ s/\s+/\t/g;$_ =~s/debris\t//;'|cut -f 1,2,4 >fragments-edit.txt 
cat fragments-edit.txt |perl fragmentbreaker.pl ../../hic/scaffolds-break/assembly.cleaned.fasta >assembly.broken.fasta
sed -i 's/:::/_/g' *tour

perl finalize-rename-assembly.pl Lnn.1TEST sample/allhic/hic-v2/groups.agp sample/allhic/hic-v2/assembly.cleaned.manualbreak1.fasta sample/allhic/hic-v2/groups.asm.fasta.rename IG_110813/plastidsearch/remove.list