README Description of files in Dryad entry doi:10.5061/dryad.k3bh40bg analysis_summary: command-line for de novo assembly, alignment and coverage estimation Read files used as input for de novo assembly and alignment, all in fastq format and zipped using gzip: Paired-end read files for sexual lineage (5 and 8 bases trimmed at 3' end, respectively): s_1_1_trimmed5nt.fq s_1_2_trimmed8nt.fq Paired-end read files for asexual lineage: s_2_1_sequence.fq s_2_2_sequence.fq Single-end read files for sexual lineage, run 1. File split in three parts and gzipped: 61V96_s_3_1_qual_trimmed.fqaa 61V96_s_3_1_qual_trimmed.fqab 61V96_s_3_1_qual_trimmed.fqac Single-end read files for asexual lineage, run 1. File split in three parts and gzipped: 61V96_s_5_1_qual_trimmed.fqaa 61V96_s_5_1_qual_trimmed.fqab 61V96_s_5_1_qual_trimmed.fqac Single-end read files for sexual lineage, run 2. File split in three parts and gzipped: s_1_1_qual_trimmed.fqaa s_1_1_qual_trimmed.fqab s_1_1_qual_trimmed.fqac Single-end read files for asexual lineage, run 2. File split in three parts and gzipped: s_2_1_qual_trimmed.fqaa s_2_1_qual_trimmed.fqab s_2_1_qual_trimmed.fqac