CAGER-misc

Miscellaneous bioinformatic tools from Laboratory “The Center of Analytical and Genetic Engineering Research”.

List of tools with links to manuals:

• pub: a script for automatic selection of sequencing barcodes;
• dedupl-fastq: the script is designed for deduplication of fastq files;
• sum-up-snv: a script for counting coverage and sigle nucleotive variants at a single specified position in SAM/BAM file;
• mean-qual: the script calculates mean quality of reads in fastq file(s);
• most-freq-subseq: the script finds N most frequently occuring subsequences of given length for each sequence in fasta file;
• NOS: the sript counts non-overalapping occurences of query sequence (and it's reverse complement "comrade") in fasta file(s);
• fasta-GC-content: the script calculates GC-content of each sequence in fasta file(s);
• fastq2fasta: the script converts fastq files to fasta format;
• fastq-read-count: the script counts amount of reads in fastq file(s);
• find-seq: the script finds fasta record(s) in fasta file by given sequence header;
• dna-summary: the script collects basic information from .dna SPAdes contigs in contigs/ directory;
• packer-dna-to-fasta: the script packs .dna SPAdes contigs in 'contigs' directory to single multi-fasta file;
• seqator: the script moves .dna SPAdes contigs with coverage less than specified one from contigs/ directory to directory cov_below_x/;
• combinator-FQ: genome assembly facilitation. This script is now moved to the separate repository: https://github.com/masikol/combinator-FQ;
• kromsatel: a tool for splitting chimeric nanopore amplicon reads. This script is now moved to the separate repository: https://github.com/masikol/kromsatel;