Salmonella
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Data
Strain:
Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150: B_SPA Salmonella typhimurium LT2 : B_STM
File locations:
/fs/ftp-cbcb/pub/data/dsommer/ /fs/szasmg/Bacteria/Salmonella/ /fs/szasmg/Bacteria/Salmonella/S_enterica_paratyphi_A/
SPA
Traces:
All directories: 103971 (unique) B_SPA : 102405 (unique) => 1566 missing
Best assembly:
/fs/szasmg/Bacteria/Salmonella/S_enterica_paratyphi_A/edit_dir/B_SPA.fasta.screen.ace.83 $ grep ^CO *ace.83 | grep -v COMM | wc -l 571
Longest contig:
$ cat B_SPA.fasta.screen.ace.83 AS 571 89509 # 571 contigs, 89509 reads ... CO Contig1368 4813926 88824 1869182 C # Contig1368 is 4813926, contains 88824 reads !!! Other Salmonella's are also 4.8M
The *.b1,*g1 reads seem to be mated!
Mate pairs:
p(.*).[bg]1 oyg(.*).[bg]1 P_AA(.*).[bg]1
Estimate lib insert sizes:
$ toAmos -ace B_SPA.fasta.screen.ace.83 $ grep -c ^rds B_SPA.afg # check if links were created $ more toAmos.error # check if there were any convertion errors $ bank-transact -b B_SPA.bnk -m B_SPA.afg -c $ bank2contig B_SPA.bnk > B_SPA.contig $ cat B_SPA.contig | grep ^# | grep -v ^## | sort # look at distances between mated reads
Create mate pair file (Bambus format, tab delimited)
$ cat B_SPA.mates library small 2000 4000 (p).* pair (p.*)\.b1$ (p.*)\.g1$ library medium 4500 5500 (oyg).* pair (oyg.*).b1$ (oyg.*).g1$ library large 35000 45000 (P_AA).* pair (P_AA.*).b1$ (P_AA.*).g1$
Rerun convertion utilities:
$ toAmos -m B_SPA.mates -ace B_SPA.fasta.screen.ace.83 -o B_SPA.afg $ bank-transact -b B_SPA.bnk -m B_SPA.afg -c