User:Dpuiu

Daniela Puiu's page

NCBI

• NCBI ; AA ; BLAST ; Microbial_Genomes ; SRA SRA_FTP ; TA ; TA_FTP ; Genomes_FTP ; Bacterial Genomes FTP ; Taxonomy CommonTree
• Complete Bacteria

Links

• Baylor
• EMBL
• EMBOSS
• Homo Sapiens Genome Projects
• JGI Microbial Genomes
• JGI Genomes Online (GOLD)
• JGI Integrated Microbial Genomes (IMG)
• Sanger
• Sanger Microbial Genomes

• ARKDB genetic maps - cow, chicken ...

Projects

DHS genomes

• Bioterrorism
• Bacillus anthracis
• Burkholderia mallei
• Burkholderia pseudomallei
• Clostridium botulinum (Hall strain A str. ATCC 3502) ; uploaded to Insignia ; (other) ; some uploaded to Insignia
• Clostridium perfringens ; some uploaded to Insignia
• Cryptosporidium hominis (test)
• Francisella tularensis OSU18 in Insignia
• Francisella tularensis some uploaded to Insignia
• Salmonella (Washington Univ in St Louis)
• Yersinia enterocolitica
• Yersinia pestis

Other

• Sequencing
• Alignment *
• CA ; Assembly
• Assemblathon
• HTS
• Comparative assemblies
• Metagenomics
• NCBI submission
• Repeat search
• Vector trimming
• Data formats

Test data sets

Sanger (1)

• 23,536 reads ; 11,652 mates; 1 lib : 4.5K mean; 7X cvg
• Location: /fs/szasmg/Bacteria/F_tularensis/TA_FTP/libs/G878A1.frg

Sanger (2)

• 100,781 reads ; 50,008 mates; 24 libs : 4.5K & 10K means; 16X cvg
• Location: /fs/szasmg/Bacteria/F_tularensis/TA_FTP/libs/G*frg

Solexa unpaired

• 2,659,250 36bp reads
• Location: /fs/szdata/Solexa/Streptococcus_suis/suisp17/strip3.fna

Solexa paired (1)

• 142,858 35bp reads;
• assemble into one 99,995 ctg/scaff by velvet
• Location /nfshomes/dpuiu/szdevel/velvet/data/test_reads.fa

Solexa paired (2)

• 92,143 35bp reads;
• assemble into 1 scaff by velvetp.sh (velveth -shortPaired)
• assemble into 5 contigs by velvet.sh (velveth)
• Location /nfshomes/dpuiu/szdevel/velvet/data/test_reads.subset.fa

Solexa & 454

• E coli Whole Genome Sequencing on 454 and Illumina
• Location /fs/szattic-asmg4/dpuiu/Ecoli