phrap_merge pipeline

sed ‘/NUCMER/’d Kall_usnused.delta > Kall_usnused.delta1
sed ‘/MD0\/work/’d Kall_usnused.delta1 > Kall_usnused.delta2

cat – all.delta.filter2 <<< “NUCMER” > all.delta.filter3

cat – all.delta.filter3 <<< “/MD0/work/aphis_phrap/aphisfinish_K31_up200.fna /MD0/work/aphis_phrap/20110718105830/t10.fna ” > all.delta.filter4

show-coords -clorH 454AllContigs_s_unal1_378.contigs.delta.filter > 454AllContigs_s_unal1_378.contigs.delta.filter.cootds3

./get_phrap_pair.py -i total.coords3 -j total.aphis.fna -o aphis.pair.info &

./singleLinkageClustering.pl aphis.pair.info aphis.pair.info.clus

./split_clus_file.pl    <dir>    <clus_file>  <total_contigfile>   <clus_splitsize>