Hey all, here at the new sub and I am very excited about it!
Gonna make a post that lists some common (free) bioinformatics tools since it always crops up.
FastUniq - Removes PCR duplicates
Skewer - Removes PCR adaptors
Musket - Error correction
There are a host of programs for static cuts, google is your friend for these.
When I say 'data format' below I am referring to the raw Fastq read stats like; base pair length, paired end data, paired end overlap, etc.
Discovar - de Bruijn graph based assembly. Very easy to run. Heavy RAM usage, moderate CPU and disk space. Requires a specific data format.
Meraculous - de Bruijn graph based assembly. Uses a ton of disk space, but not that much RAM, average CPU. Takes most data formats.
SOAP - de Bruijn graph based assembly. Tries to balance out RAM/CPU/disk space usage, takes a bit longer to run. Takes most data formats.
SGA - Takes a very long time, but accepts most data.
Abyss - de Bruijn graph based assembly. RAM skew over CPU and disk space. Takes most data formats
UCSC Genome Browser
Ensemble Genome Browser
And now we have a very basic list! Feel free to add to it/comment on it.