kmer_contig.jar quickly constricting contig profile by kmer method.
- Compress: Compressing AA sequence to contig.
| option |
Description |
| -i |
Species AA file path. |
| -k |
Setting kmer parameter value k. |
| -m |
Max add species number. |
java -Xmx9192m -jar kmer_contig.jar Compress -i /home/yangfang/PPFeature/kmer_profile/abb_seqs_class/ -k 6 -m 60
- Index: Constructing contig index.
| option |
Description |
| -i |
Species AA file path. |
| -o |
Setting store path. |
| -k |
setting kmer parameter value k. |
| -s |
Max split file number. |
| -m |
Max add species number. |
| -d |
Choose profile model (AA,CH,PO,CHP,HY) |
| --hcp |
HCP (highly conserved protein) method (default). |
| --ehcp |
HCP method with extended HCP sequences. |
| --srna |
SSU method. |
| --esrna |
SSU rRNA method with extended SSU rRNA sequences. |
java -Xmx10190m -jar kmer_contig.jar Index -i /home/yangfang/PPFeature/kmer_profile/test_jar/seq/ -k 19 -s 1 -m 4 -o /home/yangfang/PPFeature/kmer_profile/test_hy/k19_ch_index/k19_ch_split.txt -d CH
- Profile: Constructing phylogenetic profile by kmer contig.
| option |
Description |
| -i |
Species AA file path. |
| -o |
Setting store path. |
| -k |
setting kmer parameter value k. |
| -c |
The path of contig index. |
| -d |
Choose profile model (AA,CH,PO,CHP,HY) |
java -Xmx10190m -jar kmer_contig.jar Profile -i /home/yangfang/PPFeature/kmer_profile/abb_seqs500/ -k 19 -c /home/yangfang/PPFeature/kmer_profile/test_hy/k19_ch_index/ -o /home/yangfang/PPFeature/kmer_profile/test_hy/k19_ch_profile/ -d CH
- Feature: Extracting profile feature form kmer congtig profile.
| option |
Description |
| -i |
Species AA file path. |
| -o |
Setting store path. |
| -k |
setting kmer parameter value k. |
| -p |
The profile path. |
| -d |
Choose profile model (AA,CH,PO,CHP,HY) |
java -Xmx10190m -jar kmer_contig.jar Feature -i /home/yangfang/PPFeature/kmer_profile/test_jar/seq_all.fasta -k 19 -p /home/yangfang/PPFeature/kmer_profile/test_hy/k19_ch_profile/k19_ch_split0.txt -o /home/yangfang/PPFeature/kmer_profile/test_hy/k19_ch_feature/combine_contig.txt -d CH
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent