I am looking for tools to get basic statistics of contigs files from Illumina sequencing.
Hi,
1) If you are interested in the quality of the reads, you could apply fastQC.
2) There are many different tools (https://omictools.com/assembly-evaluation-category) to evaluate the quality of an assembly e.g. QUAST (http://bioinf.spbau.ru/quast). QUAST will provide some basic statistics about your assembly and run a complete evaluation of the assembly. If you are just interested in the very basic statistics of your contigs, I could send you a simple python script to calculate them.
Hi,
1) If you are interested in the quality of the reads, you could apply fastQC.
2) There are many different tools (https://omictools.com/assembly-evaluation-category) to evaluate the quality of an assembly e.g. QUAST (http://bioinf.spbau.ru/quast). QUAST will provide some basic statistics about your assembly and run a complete evaluation of the assembly. If you are just interested in the very basic statistics of your contigs, I could send you a simple python script to calculate them.
You can try contigs_statistics.py, available here: https://github.com/rbacigalupe/metagenome_assembly/blob/master/contigs_statistics.py
Hi,
As Boas mentioned you can use fastQC for the basic quality of the reads. If you want some more statistics like nucleotide distribution or histograms based on quality, distribution and clipping. use FASTX-Toolkit
http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#command_line_arguments
If you just have the raw sequence files, you can use fastqc to check quality and some other statistics. If you have a draft assembly containing contig sequences, you can use assemblathon_stats.pl to generate statistics in comparison to some other reference. http://korflab.ucdavis.edu/datasets/Assemblathon/Assemblathon2/Basic_metrics/assemblathon_stats.pl
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