The Biopython package contains high-quality, reusable modules and
scripts written in Python to make it as easy as possible to use Python
for bioinformatics. The Biopython includes the follwing: the ability
to parse bioinformatics files into python utilizable data structures,
including support for the formats such as Blast output, Clustalw,
FASTA, GenBank, PubMed and Medicine, various Expasy files, SCOP,
Rebase, UniGene, and SwissProt.
BCFtools is a program for variant calling and manipulating files in the Variant
Call Format (VCF) and its binary counterpart BCF. All commands work
transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
In order to avoid tedious repetion, throughout this document we will use "VCF"
and "BCF" interchangeably, unless specifically noted.
Most commands accept VCF, bgzipped VCF and BCF with filetype detected
automatically even when streaming from a pipe. Indexed VCF and BCF work in all
situations. Unindexed VCF and BCF and streams work in most, but not all
situations. In general, whenever multiple VCFs are read simultaneously, they
must be indexed and therefore also compressed.
Primer3 is a widely used program for designing PCR primers (PCR =
"Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool
in genetics and molecular biology. Primer3 can also design
hybridization probes and sequencing primers.
