YulongNiu / kmer_contig

kmer contig index

kmer_contig.jar quickly constricting contig profile by kmer method.

Method:

• Compress: Compressing AA sequence to contig.

options

option	Description
-i	Species AA file path.
-k	Setting kmer parameter value k.
-m	Max add species number.

Usage:

java -Xmx9192m -jar kmer_contig.jar Compress -i /home/yangfang/PPFeature/kmer_profile/abb_seqs_class/ -k 6 -m 60

Method:

• Index: Constructing contig index.

options

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.

Usage:

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

Method:

• Profile: Constructing phylogenetic profile by kmer contig.

options

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)

Usage:

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

Method:

• Feature: Extracting profile feature form kmer congtig profile.

options

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)

Usage:

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