Making sense out of CORTEX assembler

Question

[kshitijtayal]

I am under the impression that CORTEX assembles (http://cortexassembler.sourceforge.net/) a genome segment from a fastq file, without mapping to a reference genome and is used for variant calling.

I gave a a fastq which contained many reads and it returned me with this

>var_1_5p_flank length:259 average_coverage:18.47 min_coverage:1 max_coverage:46 fst_coverage:1 fst_kmer:TGAGTCACTGCATATACATACTCACAACTTT fst_r: fst_f:A lst_coverage:35 lst_kmer:ATATAATTATGAGTCATTATTTTTGTTTTGC lst_r:G lst_f:AC
TGAGTCACTGCATATACATACTCACAACTTTATTCTATAATGTAATATTCTATAAAGTAGCTGTATCAGTTTATACTTTAACCAGTAATGGACAAGATTTTCTATTACTTCCCATCTTTGTTATTACTTTTAGACTCTAACTTTTATCAGGCTCATGGATGTAAAAAGCATCTCAGGGTGGTTTTAATTTGCATTTATCTGCTCATCTATGAAGATGAGCTTCTTTTCATATAATTATGAGTCATTATTTTTGTTTTGC
>branch_1_1 length:32 average_coverage:22.81 min_coverage:14 max_coverage:32 fst_coverage:35 fst_kmer:ATATAATTATGAGTCATTATTTTTGTTTTGC fst_r:G fst_f:AC lst_coverage:47 lst_kmer:TTCTTTTGTTTATGCATTTTGCTTGTTCTAT lst_r:GT lst_f:G
ATTCTTTTGTTTATGCATTTTGCTTGTTCTAT
>branch_1_2 length:32 average_coverage:15.32 min_coverage:12 max_coverage:20 fst_coverage:35 fst_kmer:ATATAATTATGAGTCATTATTTTTGTTTTGC fst_r:G fst_f:AC lst_coverage:47 lst_kmer:TTCTTTTGTTTATGCATTTTGCTTGTTCTAT lst_r:GT lst_f:G
CTTCTTTTGTTTATGCATTTTGCTTGTTCTAT
>var_1_3p_flank length:352 average_coverage:29.58 min_coverage:3 max_coverage:53 fst_coverage:47 fst_kmer:TTCTTTTGTTTATGCATTTTGCTTGTTCTAT fst_r:GT fst_f:G lst_coverage:2 lst_kmer:ACCACTTGTTCTATTACTGCTGTAACAAATT lst_r:T lst_f:
GTCTTATTTTTCCTGTTGATTTTTGGGAGTTCATATATATTCTAAATGTATATTTATTCACTTATATATATGTTGTAAATATTACAGTTTATGATTTGTCACCTTATGATATCTTCCAAATAGAGAAGCTTTATATTTTGATGTAGTCATATGTTCATTTTTCCTCCTTAATGTTTGTTTTTCTTGGTTCTATGACCTACCAAAAGTAACAAAAATTCTCATTTATTTTTAATCTAAATGTTTTAAGTATTTTCCTGGAATTCACCTTGAATTGATTTCTATTGGAGATAGGTATCCAATCTAATTTGCCTCATATGGATAACCACTTGTTCTATTACTGCTGTAACAAATT

My question is where is the assembled genome? How to make sense of the output?

[StarCute]

Take a look at http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf. If you go to page 11, section 10.4, you will find your answer.