Just a few tools/softwares that have come handy for my research. Often times I find that the hardest part is often finding the right software to use.
Arguably one of the most used bioinformatics software. Super easy to use and install https://bedtools.readthedocs.io/en/latest/index.html
Converting SAM to BAM etc. Really useful for high-throughput sequencing data http://www.htslib.org/
Really useful command line tool in dealing with fasta/fastq files. https://bioinf.shenwei.me/seqkit/
Python library to deal with fasta files etc. Super useful if you code in python! https://biopython.org/
Lots of great bioinformatics based packages in R. I think my fav use of this is direct access to databases like Ensembl, mammalian genomes (hg19) etc. https://bioconductor.org/
Bowtie2, BWA for DNA read mapping.