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CAGER-misc

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

List of tools with links to manuals:

  • sum-up-snv: a script for counting coverage and sigle nucleotive variants at a single specified position in SAM/BAM file;
  • cigar_maplen: a script for manual inspection of structural variants, mainly for long reads. It prints which portion of a read is actually mapped, and which portions are clipped from each side.
  • samtools_setop: the script performs set operations (intersection, unuin, difference) on read IDs that are mapped to different reference positions;
  • pub: a script for automatic selection of sequencing barcodes;
  • dedupl-fastq: the script is designed for deduplication of fastq files;
  • 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;