Hum-AS-HMMER for AnVIL

This is a modified version of HumAS-HMMER. Everything you need to produce ASat annotation standart pack (except StV script) are in this repo.

Usage:

./hmmer-run.sh input_folder AS-HORs-hmmer3.3.2-120124.hmm number_of_threads
./hmmer-run_SF.sh input_folder AS-SFs-hmmer3.0.290621.hmm number_of_threads

RECOMMENDATION: If you have fasta file with few sequeces I recommend to split them into separate files with one sequence in each. So, script will proccess each sequence separately (in a loop) which will take less storage and time.

In the first commit scripts hmmer-run.sh and hmmertblout2bed.awk were the same as in the enigene repositories. After that, I added few changes (always adding comment which starts with # FEDOR). And I made two versions of hmmer-run.sh script.

For each assembly we need to generate 4 bed files: AS-HOR, AS-HOR+SF, AS-strand, AS-SF.

• AS-HOR+SF is main output of hmmer-run.sh
• AS-HOR is obtained from AS-HOR+SF by one awk command which removes SF lines (hmmer-run.sh line 63)
• AS-SF is main output of hmmer-run_SF.sh
• AS-strand is obtained from AS-SF by one awk command which changes colors (hmmer-run_SF.sh line 63)

So, to get files like in the test dir, run:

./hmmer-run.sh test/ AS-HORs-hmmer3.3.2-120124.hmm 8

Output beds: AS-HOR+SF, AS-HOR

./hmmer-run_SF.sh test/ AS-SFs-hmmer3.0.290621.hmm 8

Output beds: AS-SF, AS-strand

LAST UPDATE 01/12/2024

• updated HOR hmm was added: AS-HORs-hmmer3.3.2-120124.hmm
• color codes for new HORs were added to hmmertblout2bed.awk
• additional overlaps filtering script [overlap_filter.py] were added and implemented to hmmer-run.sh and hmmer-run_SF.sh pipelines
• scripts for converting bed to BigBed were added in bed2bb dir (to use it run ./bed2bb.sh <path/to/assembly>.fa from bed2bb dir having all beds in bed2bb dir)