Nanopore Tools
tailfindr – is an R tool that allows the direct estimation of poly(A) tail length from raw data produced by Oxford Nanopore (ONT) RNA or cDNA sequencing approaches.
CRISPR/Cas9 Genome engineering
CHOPCHOP – is a web tool for selecting the optimum target sites for CRISPR/Cas9- or TALEN-directed mutagenesis. Available as both a webtool and for the command line version.
ampliCan – is an R library for assessing cut rates using next generation sequencing. It produces summary statistics and plots. It supports mixtures of amplicons and multiplexed libraries.
Open reading frame finding and transcript data analysis
ORFik 
– an R/Bioconductor software package for transcript features, focusing on streamlining the most commonly needed transcript pipelines, with a focus on mRNAs and their open reading frames.
Ribosome profiling
shoelaces – is a tool for processing ribosome profiling data. It reads files of mapped reads and 1) filters noise, 2) produces tracks with sub-codon resolution and 3) calculate statistics over a gene set.
Motif Discovery
MoAn – Motif Annealer is a discriminatory motif discovery tool. It uses suffix arrays to rapidly contrast a positive set with a negative set to discover the maximally discriminatory position specific scoring matrix (PSSM).
JASPAR – The largest open database of transcription factor binding site motifs. Created and maintained by the Sandelin lab.