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1. sequence-stats sequence-stats Public

   Generate statistics from FASTQ and FASTA files. Also manipulate sequences such as renaming contigs and converting FASTQ to FASTA. Written in Bash. All in one place.

   Shell 10 1

2. fqtk fqtk Public

   fqtk: A toolkit to perform common tasks on FASTQ reads. Rename FASTQ identifiers, print FASTQ statistics and convert FASTQ to FASTA. This program is written in AWK and Bash.

   Shell 2

3. bioinformatics-tools bioinformatics-tools Public

   Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files

   Shell 20 5

4. R-scripts-graphing-statistics R-scripts-graphing-statistics Public

   My R scripts, primarily R plotting scripts + some genomics software including 16S rRNA metataxnomics and RNAseq

   R 10 2

5. bactspeciesID bactspeciesID Public

   Fast microbial species identification (16S rRNA gene-based approach) and contamination check using whole genome assemblies

   Shell 3 2

6. fastq-info fastq-info Public

   Calculate fastq reads and sequencing coverage

   Shell 14 1