_contig_info_ is a command line program written in [Bash](https://www.gnu.org/software/bash/) for quickly estimating several standard descriptive statistics from FASTA-formatted contig files inferred by _de novo_ genome assembly methods.
_contig_info_ is a command line program written in [Bash](https://www.gnu.org/software/bash/) for quickly estimating several standard descriptive statistics from FASTA-formatted contig files inferred by _de novo_ genome assembly methods.
Estimated statistics are sequence number, residue counts, AT- and GC-content, sequence lengths, [auN](https://lh3.github.io/2020/04/08/a-new-metric-on-assembly-contiguity)(also called E-size, Salzberg et al. 2012), [N50](https://en.wikipedia.org/wiki/N50,_L50,_and_related_statistics)(Lander et al. 2001), [NG50](https://en.wikipedia.org/wiki/N50,_L50,_and_related_statistics)(Earl et al. 2011), and the related N75, NG75, N90, NG90, L50, LG50, L75, LG75, L90, LG90.
Estimated statistics are sequence number, residue counts, AT- and GC-content, sequence lengths, [auN](https://lh3.github.io/2020/04/08/a-new-metric-on-assembly-contiguity)(also called E-size, Salzberg et al. 2012), [N50](https://en.wikipedia.org/wiki/N50,_L50,_and_related_statistics)(Lander et al. 2001), [NG50](https://en.wikipedia.org/wiki/N50,_L50,_and_related_statistics)(Earl et al. 2011), and the related N(G)75, N(G)G90, L(G)50, L(G)75, L(G)90.
_contig_info_ can also estimates nucleotide content statistics for each contig sequence.
## Installation and execution
## Installation and execution
Give the execute permission to the file `contig_info.sh` by typing:
Give the execute permission to the file `contig_info.sh` by typing:
```bash
```bash
chmod +x contig_info.sh
chmod +x contig_info.sh
...
@@ -29,6 +30,8 @@ Run _contig_info_ without option to read the following documentation:
...
@@ -29,6 +30,8 @@ Run _contig_info_ without option to read the following documentation:
than this cutoff will be discarded (default: 1)
than this cutoff will be discarded (default: 1)
-g <int> expected genome size for computing auNG and {N,L}G{50,75,90}
-g <int> expected genome size for computing auNG and {N,L}G{50,75,90}
values instead of auN and {N,L}{50,75,90} ones, respectively
values instead of auN and {N,L}{50,75,90} ones, respectively
-r residue content statistics for each contig sequence instead of
Finally, the option `-g` can be used to set an expected genome size for obtaining auNG and {N,L}G{50,75,90} statistics instead of auN and {N,L}{50,75,90} ones:
The option `-g` can be used to set an expected genome size for obtaining auNG and {N,L}G{50,75,90} statistics instead of auN and {N,L}{50,75,90} ones:
Note that the last column `Pval` assesses the GC-content adequation between each contig and the longest one.
When _Pval_ is close to 0, then the %GC of the corresponding contig is significantly different to the %GC of the longest one.
This _p_-value can be used as an indicator when searching for particular replicons (e.g. plasmids, mitochondrion) or artefactual contigs, as such sequences often induce specific nucleotide compositions.
Indeed, when considering a FASTA file outputted by a _de novo_ assembly program, the longest contig generally does not correspond to such replicon(s), therefore giving a good approximation of the expected GC-content within the hole chromosome.
## References
## References
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B (2011) _Assemblathon 1: a competitive assessment of de novo short read assembly methods_. **Genome Research**, 21(12):2224-2241. [doi:10.1101/gr.126599.111](https://genome.cshlp.org/content/21/12/2224).
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B (2011) _Assemblathon 1: a competitive assessment of de novo short read assembly methods_. **Genome Research**, 21(12):2224-2241. [doi:10.1101/gr.126599.111](https://genome.cshlp.org/content/21/12/2224).
