Note: Unless otherwise mentioned, adapter sequences in this directory should be trimmed to the right.  For BBDuk, that means using the flag "ktrim=r".

contents.txt
This file.

remote_files.txt
A list of remote files that are too big to package with BBTools, but are available for download from my google drive.

adapters.fa
All adapters in one file, provided for convenience.

adapters_no_transposase.fa.gz
This should be used instead of adapters.fa when trimming Nextera Long-Mate Pair libraries.

sequencing_artifacts.fa.gz
Artificial contaminants filtered by JGI.

truseq.fa.gz
Illumina Truseq DNA adapters.

truseq_rna.fa.gz
Illumina Truseq RNA adapters.

nextera.fa.gz
Illumina Nextera adapter sequences.

nextera_LMP_adapter.fa.gz
Illumina Nextera long-mate-pair adapters.

nextera_LMP_linker.fa.gz
Illumina Nextera sequence that joins the circularized DNA in LMP libraries.  This should be handled specially, e.g. with SplitNexteraLMP.

phix174_ill.ref.fa.gz
Illumina PhiX spike-in reference genome, for filtering with BBDuk or mapping for quality metrics.

phix_adapters.fa.gz
A set of adapters found on a PhiX library; may be subject to change.

sample1.fq.gz
sample2.fq.gz
Sample read pairs for testing whether the programs are working.  These are from PhiX.

primes.txt.gz
A prime selection of numbers.  These are used for hash functions.

mtst.fa
Some spike-ins used at JGI for metatranscriptomes.

kapatags.L40.fa
Some spike-in sequences intended for use in detecting cross-contamination.

blacklist_nt_merged.sketch
A blacklist of uninformative keys from nt, used by SendSketch.

blacklist_silva_merged.sketch
A blacklist of uninformative keys from Silva, used by SendSketch.

blacklist_refseq_merged.sketch
A blacklist of uninformative keys from RefSeq, used by SendSketch.

blacklist_img_species_300.sketch
A blacklist of uninformative keys from IMG, used by CompareSketch at JGI (there is no current IMG server).

small.fa
A subset of sequencing_artifacts.fa.gz shorter than 31bp.  This is used for an optional 2nd filtering pass with a shorter kmer because k=31 will not detect these artifacts.

lambda.fa.gz
Sequence of a lambda phage commonly used as a spike-in or for testing sequencing machines.

pjET1.2.fa
A cloning vector that is sometimes present as a contaminant sequence.

polyA.fa.gz
31 A's in a row.  Potentially useful for filtering RNA-seq data, though note that BBDuk now has a "trimpolya" flag.

favicon.ico
For the taxonomy server.

16S_consensus_sequence.fa
These files contain consensus sequences of various conserved RNAs (rRNAs and tRNAs) from different clades.

model.pgm
Prokaryotic gene model, used by CallGenes and BBSketch in protein mode.

