文件列表:

CHANGELOG.md
NOS.py
dedupl-fastq.py
dna-summary.py
fasta-GC-content.py
fastq-read-count.py
fastq2fasta.py
find-seq.py
mean-qual.py
most-freq-subseq.py
packer-dna-to-fasta.py
pub.R
seqator.py
sum_up_snv.awk

# CAGER-misc Miscellaneous bioinformatic tools from [Laboratory](https://mbio.bas-net.by/cager/en/) “The **C**enter of **A**nalytical and **G**enetic **E**ngineering **R**esearch”. List of tools with links to manuals: - [pub](https://www.github.com/masikol/cager-misc/wiki/pub): a script for automatic selection of sequencing barcodes; - [dedupl-fastq](https://www.github.com/masikol/cager-misc/wiki/dedupl-fastq): the script is designed for deduplication of fastq files; - [sum-up-snv](https://www.github.com/masikol/cager-misc/wiki/sum-up-snv): a script for counting coverage and sigle nucleotive variants at a single specified position in SAM/BAM file; - [mean-qual](https://www.github.com/masikol/cager-misc/wiki/mean-qual): the script calculates mean quality of reads in `fastq` file(s); - [most-freq-subseq](https://www.github.com/masikol/cager-misc/wiki/most-freq-subseq): the script finds N most frequently occuring subsequences of given length for each sequence in fasta file; - [NOS](https://www.github.com/masikol/cager-misc/wiki/NOS): the sript counts non-overalapping occurences of query sequence (and it's reverse complement "comrade") in `fasta` file(s); - [fasta-GC-content](https://www.github.com/masikol/cager-misc/wiki/fasta-GC-content): the script calculates GC-content of each sequence in `fasta` file(s); - [fastq2fasta](https://www.github.com/masikol/cager-misc/wiki/fastq2fasta): the script converts `fastq` files to `fasta` format; - [fastq-read-count](https://www.github.com/masikol/cager-misc/wiki/fastq-read-count): the script counts amount of reads in `fastq` file(s); - [find-seq](https://www.github.com/masikol/cager-misc/wiki/find-seq): the script finds fasta record(s) in `fasta` file by given sequence header; - [dna-summary](https://www.github.com/masikol/cager-misc/wiki/dna-summary): the script collects basic information from `.dna` [SPAdes](http://cab.spbu.ru/software/spades/) contigs in `contigs/` directory; - [packer-dna-to-fasta](https://www.github.com/masikol/cager-misc/wiki/packer-dna-to-fasta): the script packs `.dna` [SPAdes](http://cab.spbu.ru/software/spades/) contigs in 'contigs' directory to single multi-fasta file; - [seqator](https://www.github.com/masikol/cager-misc/wiki/seqator): the script moves `.dna` [SPAdes](http://cab.spbu.ru/software/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](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](https://github.com/masikol/kromsatel);

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