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Jennifer Shelton edited results.tex
over 8 years ago
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\subsection{Data}
Fasta-O-Matic and two pther common FASTA tools that can wrap a FASTA file were tested on the Vicugna_pacos-2.0.1 whole genome shotgun sequence scaffolds because the 2.17 Gb
Vicugna pacos \textit{Vicugna pacos} genome is large (> 1 Gb) and has many scaffolds (276727). The large genome size and high number of individual sequences should approximate a typical large FASTA file. The FASTA file was downloaded from the NCBI FTP as
NW_005882702.1 NW\_005882702.1 Vicugna pacos isolate Carlotta (AHFN-0088)
Vicugna_pacos-2.0.1 Vicugna\_pacos-2.0.1 assembly scaffolds.
An additional unwrapped sequence was added to the end of the file. This sequence was also missing a newline. Each FASTA record in the file also had spaces within the text of the headers.
Additional simulated FASTA record:
\begin{verbatim}
>NW_000000000.0 Vicugna pacos isolate Carlotta (AHFN-0088) FAKE genomic scaffold, Vicugna_pacos-2.0.1 Scaffold-, whole genome shotgun sequence
ATACAACCATAAAGGTGCTATTCAGTCCATGGTTACAGGACATAACTACAACACACACCCACGTACACATGCGCATGCGCATGCACACACCCACGTACACGTACACGTACGCATACACACCCACGTACACGTACACGTACGCATACACACCCACGTACACGTACACGTACGCATACACACCCACGTACACGTACACGTACGCATACACACCCACGTACACGTACACGTACGCATACACACCCACGTACGCACACACGTACACGTGTAGGCACGCATTTAGCAAGTATTTAGCTTGCTTAAACAAACCCCCCCTACCCCCCACGAGCCCCACCTTATATACCAGACAGTCTTGCCAAACCCCAAAAACAAGACATAGCGCATAAGCTATAGAACCCGGACAAACCTTTGCCCACAAACCCAACTTCTTAAATAATCACATGGCCAAATCGTACCAATGTGTTACTCTAGTATATTAAAAATATACAGACAGCTATCTCCCTAGATCCGCCAAAATTTTTAAAACAGAATTCAACAACCTTTTTAATGGCACCCCCCCCCCCCATAAATGACC
\end{verbatim}
Fully re-formatted simulated FASTA record:
\begin{verbatim}
>NW_000000000.0_Vicugna_pacos_isolate_Carlotta_(AHFN-0088)_FAKE_genomic_scaffold,_Vicugna_pacos-2.0.1_Scaffold-,_whole_genome_shotgun_sequence
ATACAACCATAAAGGTGCTATTCAGTCCATGGTTACAGGACATAACTACAACACACACCC
ACGTACACATGCGCATGCGCATGCACACACCCACGTACACGTACACGTACGCATACACAC
CCACGTACACGTACACGTACGCATACACACCCACGTACACGTACACGTACGCATACACAC
CCACGTACACGTACACGTACGCATACACACCCACGTACACGTACACGTACGCATACACAC
CCACGTACGCACACACGTACACGTGTAGGCACGCATTTAGCAAGTATTTAGCTTGCTTAA
ACAAACCCCCCCTACCCCCCACGAGCCCCACCTTATATACCAGACAGTCTTGCCAAACCC
CAAAAACAAGACATAGCGCATAAGCTATAGAACCCGGACAAACCTTTGCCCACAAACCCA
ACTTCTTAAATAATCACATGGCCAAATCGTACCAATGTGTTACTCTAGTATATTAAAAAT
ATACAGACAGCTATCTCCCTAGATCCGCCAAAATTTTTAAAACAGAATTCAACAACCTTT
TTAATGGCACCCCCCCCCCCCATAAATGACC
\end{verbatim}
\subsection{Data}
Reference from the NW_005882702.1 Vicugna pacos isolate Carlotta (AHFN-0088) Vicugna_pacos-2.0.1 whole genome shotgun sequence
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N50 (bp): 7263804
Total length (bp) : 2.17
The number of contigs is: 276727