1.0.190426ac

README.md

 # contig_info
 
-_contig_info_ is a command line program written in [Bash](https://www.gnu.org/software/bash/) that allows estimating several standard descriptive statistics from a FASTA-formatted contig file inferred by a _de novo_ genome assembly method. Estimated statistics are sequence number, residue counts, sequence length distribution, N50 (Lander et al. 2001), NG50 (Earl et al. 2011), and its related N75, NG75, N90, and NG90.
+_contig_info_ is a command line program written in [Bash](https://www.gnu.org/software/bash/) that allows several standard descriptive statistics to be quickly estimated 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, N50 (Lander et al. 2001), NG50 (Earl et al. 2011), and the related N75, NG75, N90, NG90, L50, LG50, L75, LG75, L90, LG90.
 
 ## Installation and execution
 
@@ -18,20 +19,118 @@ and launch it with the following command line model:
 Launch _contig_info_ without option to read the following documentation:
 
 ```
- USAGE:  contig_info.sh  [options]  <contig_file> 
+ USAGE:  contig_info.sh  [options]  <contig_files>
 
   where 'options' are:
 
    -m <int>    minimum contig length;  every contig sequence of length
-               shorter than this cutoff will be discarded (default: 0)
-   -g <int>    expected genome size  for computing NG50, NG75 and NG90
-               values instead of N50, N75 and N90 ones, respectively
-   -d          print contig sequence length distribution
-   -l          print length of each contig sequence
-   -r          print residue counts
+               shorter than this cutoff will be discarded (default: 1)
+   -g <int>    expected  genome  size  for  computing {N,L}G{50,75,90}
+               values instead of {N,L}{50,75,90} ones, respectively
    -t          tab-delimited output
 ```
 
+## Examples
+
+The following [Bash](https://www.gnu.org/software/bash/) command lines allows the genome sequences of the 5 _Mucor circinelloides_ strains 1006PhL, CBS 277.49, WJ11, B8987 and JCM 22480 to be downloaded from the [NCBI genome repository](https://www.ncbi.nlm.nih.gov/genome):
+```bash
+NCBIFTP="wget -q -O- https://ftp.ncbi.nlm.nih.gov/sra/wgs_aux/"; Z=".1.fsa_nt.gz";
+echo -e "1006PhL\tAOCY01\nCBS277.49\tAMYB01\nWJ11\tLGTF01\nB8987\tJNDM01\nJCM22480\tBCHG01" |
+  while read -r s a; do echo -n "$s ... ";$NCBIFTP${a:0:2}/${a:2:2}/$a/$a$Z|zcat>Mucor.$s.fasta;echo "[ok]";done
+```
+
+The following command line allows the script `contig_info.sh` to be launched to analyze the first downloaded file _Mucor.1006PhL.fasta_:
+```bash
+./contig_info.sh  Mucor.1006PhL.fasta
+```
+leading to the following standard output:
+```
+File                           Mucor.1006PhL.fasta
+
+Number of sequences            1459
+
+Residue counts:
+  Number of A's                10320010  30.23 %
+  Number of C's                6747611  19.76 %
+  Number of G's                6731530  19.72 %
+  Number of T's                10335465  30.27 %
+  Number of N's                0  0 %
+  Total                        34134616
+
+  %AT                          60.52 %
+  %GC                          39.48 %
+
+Sequence lengths:
+  Minimum                      410
+  Quartile 25%                 1660
+  Median                       6176
+  Quartile 75%                 37608
+  Maximum                      213712
+  Average                      23395.89
+
+Contiguity statistics:
+  N50                          58982
+  N75                          36291
+  N90                          18584
+  L50                          194
+  L75                          376
+  L90                          562
+```
+
+The same results could be outputted in tab-delimited format with the following command line:
+```bash
+./contig_info.sh  -t  Mucor.1006PhL.fasta
+```
+
+```
+#File               Nseq   Nres     A        C       G       T        N    %A     %C     %G     %T     %N   %AT    %GC     Min   Q25   Med   Q75   Max    Avg       N50   N75   N90   L50 L75 L90
+Mucor.1006PhL.fasta 1459   34134616 10320010 6747611 6731530 10335465 0    30.23% 19.76% 19.72% 30.27% 0%   60.52% 39.48%  410   1660  6176  37608 213712 23395.89  58982 36291 18584 194 376 562
+```
+
+Of note, the five downloaded FASTA files could be analyzed with a single command line:
+```bash
+./contig_info.sh  -t  Mucor.*.fasta
+```
+
+```
+#File                 Nseq   Nres      A        C       G       T        N       %A     %C     %G     %T     %N    %AT    %GC     Min   Q25   Med    Q75     Max     Avg         N50      N75     N90      L50 L75 L90
+Mucor.1006PhL.fasta   1459   34134616  10320010 6747611 6731530 10335465 0       30.23% 19.76% 19.72% 30.27% 0%    60.52% 39.48%  410   1660  6176   37608   213712  23395.89    58982    36291   18584    194 376 562
+Mucor.B8987.fasta     2210   36700617  11096810 7247117 7233795 11122895 0       30.23% 19.74% 19.71% 30.30% 0%    60.55% 39.45%  206   839   2482   20727   258792  16606.61    58460    30025   13274    193 416 674
+Mucor.CBS277.49.fasta 21     36567582  10571030 7715901 7705901 10574750 0       28.90% 21.10% 21.07% 28.91% 0%    57.83% 42.17%  4155  41542 934259 3187354 6050249 1741313.42  4318338  3096690 1074709  4   7   9
+Mucor.JCM22480.fasta  401    36616466  10586281 6882218 6899109 10581984 1659222 28.91% 18.79% 18.84% 28.89% 4.53% 60.57% 39.43%  1038  4814  50332  135940  659822  91312.88    197059   109360  63107    61  121 183
+Mucor.WJ11.fasta      2519   33065171  9974064  6559358 6556539 9975210  0       30.16% 19.83% 19.82% 30.16% 0%    60.34% 39.66%  430   3275  7692   18010   118704  13126.30    24148    12884   5672     429 898 1455
+```
+
+The tab-delimited output format could be useful for focusing on specific fields like, e.g. the six contiguity statistics:
+```bash
+./contig_info.sh  -t  Mucor.*.fasta  |  cut -f1,22-
+```
+
+```
+#File                 N50      N75     N90      L50  L75  L90
+Mucor.1006PhL.fasta   58982    36291   18584    194  376  562
+Mucor.B8987.fasta     58460    30025   13274    193  416  674
+Mucor.CBS277.49.fasta 4318338  3096690 1074709  4    7    9
+Mucor.JCM22480.fasta  197059   109360  63107    61   121  183
+Mucor.WJ11.fasta      24148    12884   5672     429  898  1455
+```
+
+
+Finally, the option -g could be used to set an expected genome size for obtaining {N,L}G{50,75,90} statistics instead of {N,L}{50,75,90} ones:
+```bash
+./contig_info.sh  -t  -g 36000000  Mucor.*.fasta | cut -f1,22-
+```
+
+```
+#File                 N50      N75     N90      L50  L75  L90  ExpSize
+Mucor.1006PhL.fasta   57499    32472   7652     210  417  692  36000000
+Mucor.B8987.fasta     59771    30857   15730    187  399  631  36000000
+Mucor.CBS277.49.fasta 4318338  3096690 1074709  4    7    9    36000000
+Mucor.JCM22480.fasta  197663   113006  69531    59   117  175  36000000
+Mucor.WJ11.fasta      21799    9865    2445     493  1092 2146 36000000
+```
+
+
 ## 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).