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Miscellaneous bioinformatic tools fromLaboratory “TheCenter ofAnalytical andGeneticEngineeringResearch”.

List of tools with links to manuals:

• sum-up-snv: a script for counting coverage and single nucleotide 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, union, difference) on read IDs that are mapped to arbitrary reference positions;
• gla-glar: “GLAde GLARer”: the script finds long intergenic and inter-CDS regions in GenBank files;
• AAI-taxon.sh(Help page is yet to be done): the script calculates Average Amino acid Identities between a query genome and all type strain genomes of a given taxon;
• 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 infastq 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") infasta file(s);
• fasta-GC-content: the script calculates GC-content of each sequence infasta file(s);
• fastq2fasta: the script convertsfastq files tofasta format;
• fastq-read-count: the script counts amount of reads infastq file(s);
• find-seq: the script finds fasta record(s) infasta file by given sequence header;
• dna-summary: the script collects basic information from.dnaSPAdes contigs incontigs/ directory;
• packer-dna-to-fasta: the script packs.dnaSPAdes contigs in 'contigs' directory to single multi-fasta file;
• seqator: the script moves.dnaSPAdes contigs with coverage less than specified one fromcontigs/ directory to directorycov_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;