- rust samtools genomecapture.
- give the id list, reference genome, upstream and downstream and extracts the reference genome portion for the genome browser.
- rust-samtools-genome-capture: takes a genome alignment files, a reference fasta file, the upstream and the downstream regions
- targetd capture assay development for taking reads from HybSeq.
- general note: Incase of Golang and RUST, please see the last commit message and if it says compiled binary then it is completed or else still in development version.
cargo build
λ gauravsablok rust-samtools-genomecapture → λ git main* → ./target/debug/rust-samtools-genome-capture -h
Usage: rust-samtools-genome-capture <ALIGNMENT_ARG> <IDLIST_ARG> <FASTA_ARG> <UPSTREAM_ARG> <DOWNSTREAM_ARG> <READLENGTH_ARG>
Arguments:
<ALIGNMENT_ARG> please provide the path to the alignment file
<IDLIST_ARG> please provide the id list for the specific region
<FASTA_ARG> please provide the fasta file used for the reference alignment
<UPSTREAM_ARG> please provide the upstream add from the sam alignments to be extracted
<DOWNSTREAM_ARG> please provide the downstream add from the sam alignments to be extracted
<READLENGTH_ARG> please provide the readlength of the sequencing reads
Options:
-h, --help Print help
-V, --version Print version
- how to run the binary
./rust-samtools-genome-capture ./sample-files/Col0_C1.100k_selected.sam ./sample-files/idlist.txt ./sample-files/sample-fasta.fasta 5 10
``
- result from the rust-samtools-genome-capture
- selected-ids-downstream.fasta - downstream for those ids
- selected-ids-reads.fasta - reads aligned to those ids.
- selected-ids-upstream.fasta - upstreams for those ids.
- selected-ids-upstream-region-downstream.fasta - upstream-region -downstream for those ids.
Gaurav Sablok