Simplify remove_files function

Catch RemoteDisconnected errors and refactor download_taxonomy function

Make sure that MD5 checks are performed on fresh downloads

Do not use multithreading when fetching links from NCBI API

Fix an issue causing k2mask to read only from stdin

General improvements to file downloads

Create directory structure before attempting to open file

Remove many thread option from inspect command

Commit VERSION file

Update API endpoints and make sure that workers respect NCBI rate limits

Add --version flag to k2

Use absolute paths when processing downloaded files

Fix an issue causing k2 to generate empty library files for plasmid, …

Fix an issue causing plasmid download to falsely error out

Fix memory leaks and crashes in previous release

Fix an issue causing kraken2 to incorrectly format (un)classified ouput

Update documentation for release of v2.1.4

Fix typo

Minor cleanup to source code

Report a warning instead of crashing when accession2taxid files conta…

Parse storage units

Update SILVA version to 138.2

Speed up processing of sequences across all kraken2 operations

Fetch accessions directly instead of using the NCBI API

Speed up decompression using zlib, make downloading large amounts of …

Remove taxids from seqid2taxid.map file that are not present in the n…

Fix an issue causing k2 to not find a database when a relative path i…

Fix issue causing k2 to crash while comparing mtimes

Minor change to how prelim.map and seqid2taxid are generated

Add progress bar when building database