v0.5.4

FCS-GX

• Consume input file directly with gzip/minizip as potential fix for “No data available” errors
• Added memory stats and SIGKILL/SIGTERM error reporting in debug mode
• Changed maximum allowable sequence length to 2147483000
• Added contaminated database sequences to exclusion list
• Fixed error where synthetic phiX was not called as contaminant in metagenomes
• Sensitivity and specificity improvements

FCS-adaptor

• Updates to adaptor databases to match NCBI internal screening

v0.5.0

FCS-GX

• Bioconda release (https://bioconda.github.io/recipes/ncbi-fcs-gx/README.html)
• Added feature to avoid calling eutils unless absolutely necessary, i.e. can skip if --species or --out-basename is not specified.
• Support seq-ids that include ~
• For fcs clean genome, added option to split on FIX actions
• Removed trailing newlines in output FASTA generated by gx clean genome
• Improved error message for duplicate seqids in GX
• Print out a helpful message when gx errors out due to too short assembly
• Removed some more contaminated sequences from GXDB
• Expanded the Fungi report category in GX to include Mucoromycota and Zoopagomycota
• Reduced GX false positives in eukaryote repeat regions
• Increased GX score thresholds required for calling intra-superkingdom contamination
• Added documentation on how to specify host for metagenome
• Updated documentation for fcs clean genome with updated examples

FCS-adaptor

• New adaptor sequences from Pacific Biosciences, Oxford Nanopore Technologies, and Illumina
• Excluded four transposase sequences in the prokaryotes adaptors file
• Added option to split on ACTION_TRIM ranges from adaptor hits

v0.4.0

0.4.0 March 8 2023

GX:
GX database also available in S3
Runner improvements, including database download and run FCS as two separate commands
Incremental improvements in the GX algorithm
Added ability to clean the contaminant sequences from the assembly
Added ability to save the contaminant sequences into a file
Various bug fixes

v0.3.0-beta

0.3.0 28 Nov 2022

GX:
Progress bar improvements
Shift to CLI11 command line parsing
Various algorithm improvements to reduce false positive rate
Taxify command line fixes
Added missing conditional for split-fasta mode
Added initial support for metagenomics
Various bug fixes

Adaptor:
Recompress file if the extension is .gz
Too many Ns gives warning instead of error
Run docker with --rm
Expose debug mode

v0.2.3-beta

0.2.3 September 7, 2022

GX:
added --use-logfile to direct stdout and stderr to a file
added headers to the contamination report table
improved stdout messaging
added progress bar for database download
added --env-file to allow users to control env vars
added bash to the Docker and Singularity images

Adaptor:
added bash to the Docker and Singularity images

v0.2.2-beta

0.2.2 August 2, 2022

FCS-GX
Support copy from disk store to shared mem without internet

FCS-Adaptor
No changes

v0.2.1-beta

0.2.1: July 27, 2022

FCS-adaptor

• added Singularity support

FCS-GX

• new database released, with improved coverage of prokaryotes unicellular eukaryotes
• added categorization of contaminants by kingdom, and reduced likely false positives from closer taxonomic divisions
• revised name from FCS-genome
• improved aria2 database download behavior

Documentation

• migrated to GitHub
• added Google Cloud quickstart