Bioinformatics

Essential tools

• FASTA/Q files - https://github.com/lh3/seqtk
• BED files - https://github.com/arq5x/bedtools2
• SAM/BAM files - https://github.com/samtools
• FASTQ files - https://github.com/OpenGene/fastp
• V/BCF files - https://github.com/samtools/bcftools
• CSV files - https://csvkit.readthedocs.io/en/latest/
• Multiple sequence alignment -
• Assembly toolkit - http://cab.spbu.ru/software/spades/

http://mama.indstate.edu/users/ice/tree/

Conda environment file

name: seq
channels:
  - bioconda
  - anaconda
  - conda-forge
  - defaults
dependencies:
  - bwa
  - samtools
  - bedtools
  - deeptools
  - minimap2
  - fastp
  - parallel
  - seqtk
  - bcftools
  - vcftools
  - csvkit

Licensing

• Picard - MIT License
• RNA-SeQC - BSD 3-clause license
• RSEM - GNU GPL
• samtools - The MIT/Expat License