Can anyone suggest a command line to generate reference assembly of 17 million solexa 50 bp reads on reference genome index (index generated from fasta file) that can be used for SNP discovery.
Thanks.
Thanks.
-
-
hi
what is your genome assembly. you could download almost any pre-built indexes directly from this link. Hope this helps.After unzipping the index file run the bash command inside the folder some thing like genome.sh(make_hg18.sh) and it will create a fasta files like chr1.fa to chrY.fa. and if you need a single big FASTA file that include all chromosome info use this simple command
cat chr1. fa chr2.fa ....chrY.fa >>hg18.fa
HTH
repine
-
NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM -
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM
Comment