Global option Value Description
ALIGNED_CHECK 10 Min equal aligned part
ALIGNER_GAP_PENALTY 2 Gap penalty for aligner
ALIGNER_GAP_RANGE 15 Max distance from main diagonal of considered states of pair alignment
ALIGNER_MAX_ERRORS 11 Max number of errors in pair alignment
ALIGNER_MISMATCH_PENALTY 1 Mismatch penalty for aligner
ANCHOR_FP 0.1 Probability of false positive in Bloom filter
ANCHOR_SIZE 20 Anchor size (AnchorFinder)
BLASTALL_CMD blastall -p blastn -m 8 -d {bank} -i {in} -e {evalue} -a {workers} -F {F} > {out} blastall command
BLASTALL_EXE blastall blastall executable (legacy blast)
BLASTALL_TMP {BLASTALL} -p blastn -m 8 -d {bank} -i {in} -e {evalue} -a {workers} -F {F} > {out} blastall command template (legacy blast)
BLASTN_CMD blastn -task blastn -outfmt 6 -db {bank} -query {in} -evalue {evalue} -num_threads {workers} -dust {F} > {out} blastn command
BLASTN_EXE blastn blastn executable (blast+)
BLASTN_TMP {BLASTN} -task blastn -outfmt 6 -db {bank} -query {in} -evalue {evalue} -num_threads {workers} -dust {F} > {out} blastn command template (blast+)
BLAST_DUST 0 E-value filter out low complexity regions
BLAST_EVALUE 0.001 E-value filter for blast
BLAST_PLUS 0 Use blast+ instead of blast
BLOCKS_IN_GROUP 10 Number of blocks processing at once (BlocksJobs)
BOUNDARIES_MIN_DISTANCE 30 Min distance between fragment boundaries (overlaps resolver 2)
CONFIG0 LOCAL_CONF Config file 0
CONFIG1 Config file 1
CONFIG2 /etc/npge.conf Config file 2
CONFIG3 Config file 3
CONFIG4 ~/.npge.conf Config file 4
CONFIG5 Config file 5
CONFIG6 ENV Config file 6
CONFIG7 Config file 7
CONFIG8 LOCAL_CONF Config file 8
CONFIG9 Config file 9
DEV_NULL NUL Null device
EXPANDER_BATCH 100 Pair alignment expander batch size
EXPANDER_MAX_OVERLAP 200 Neighbors overlaps when expanding
EXTERNAL_ALIGNER_CMD mafft --quiet --retree 1 --maxiterate 1 %1% > %2% ExternalAligner command Use %1% as input of aligner, %2% as output
FALLBACK_ALIGNER mafft,muscle,similar Try external aligner; if fails, use similar aligner
FORMATDB_CMD formatdb -l {nul} -p F -i {in} -n {bank} formatdb command
FORMATDB_EXE formatdb formatdb executable (legacy blast)
FORMATDB_TMP {FORMATDB} -l {nul} -p F -i {in} -n {bank} formatdb command template (legacy blast)
GAP_CHECK 2 Min number of equal columns after single gap
JOINER_GAP_RATIO 1.5 Max allowed ratio of gaps' lengths (inside a block)
JOINER_MAX_DIST 100 Maximum distance between joint fragments
JOINER_RATIO_TO_FRAGMENT 0.5 Max allowed gap length to fragment length ratio
LOCAL_CONF npge.conf Local config file name
LOG_TO :cerr Where to write log messages
MAFFT_CMD mafft --quiet --retree 1 --maxiterate 1 %1% > %2% Mafft command
MAFFT_EXE mafft Mafft executable
MAFFT_TMP {MAFFT} --quiet --retree 1 --maxiterate 1 %1% > %2% Mafft command template
MAKEBLASTDB_CMD makeblastdb -dbtype nucl -out {bank} -in {in} -logfile {nul} makeblastdb command
MAKEBLASTDB_EXE makeblastdb makeblastdb executable (blast+)
MAKEBLASTDB_TMP {MAKEBLASTDB} -dbtype nucl -out {bank} -in {in} -logfile {nul} makeblastdb command template (blast+)
MAX_ANCHOR_FRAGMENTS 100000 Maximum number of anchors fragments
MAX_EVALUE 0.001 Maximum acceptable e-value
MAX_GAPS 0.2 Maximum acceptable percentage of gap positions
MAX_MATCHES 1000 Maximum number of matches (FragmentFinder)
MAX_SPREADING 0.2 Maximum acceptable distance spreading of fragments in block
MAX_TAIL 3 Max length of tail (MoveGaps)
MAX_TAIL_TO_GAP 1 Max tail length to gap length ratio (MoveGaps)
META_ALIGNER similar Default aligner
MIN_IDENTITY 0.9 Minimum acceptable identity of block
MIN_LENGTH 100 Minimum acceptable length of fragment
MISMATCH_CHECK 1 Min number of equal columns after single mismatch
MUSCLE_CMD muscle -quiet -in %1% -out %2% -maxiters 1 -diags1 Muscle command
MUSCLE_EXE muscle Muscle executable
MUSCLE_TMP {MUSCLE} -quiet -in %1% -out %2% -maxiters 1 -diags1 Muscle command template
NPGE_DEBUG 0 Debug mode
SPLIT_REPEATS_MIN_DIAGNOSTIC_MUTATIONS 2 Min number of diagnostic mutations in part of splitted block
SPLIT_REPEATS_MIN_MUTATIONS 4 Min number of mutations in candidate block to be splited
TIMING 0 Log begin/end of calls and final time summary
WORKERS -1 Number of threads (-1 = number of cores)