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.
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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
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