| 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) |