I just completed my first genome assembly using abyss (made from 1 set of paired-end files, 1 single end file, and 7 mate pair sets). Abyss creates a large number of output files, and what I'd like to do now is blast my assembly to remove contigs that are potentially there due to contamination. Nevertheless, I am confused about what .fa file represents my final assembly (as there are 13 different .fa files (see below)). What do the numbered files represent (bowfin-1.fa, bowfin-2.fa, etc.)? Will I need to combine these for a final assembly (assuming I want to eventually map reads to the assembly from different individuals and get a .vcf file for pop gen analysis)? I'm just a little confused as to why there are so many output files...

bowfin-1.dot     bowfin-6.dot          coverage.hist
bowfin-1.fa      bowfin-6.fa           mpc-6.dist.dot
bowfin-1.path    bowfin-6.path         mpc-6.hist
bowfin-2.dot     bowfin-6.path.dot     mpd-6.dist.dot
bowfin-2.dot1    bowfin-7.dot          mpd-6.hist
bowfin-2.fa      bowfin-7.fa           mpe-6.dist.dot
bowfin-2.path    bowfin-7.path         mpe-6.hist
bowfin-3.dist    bowfin-8.dot          mpf-6.dist.dot
bowfin-3.dot     bowfin-8.fa           mpf-6.hist
bowfin-3.fa      bowfin-bubbles.fa     mpg-6.dist.dot
bowfin-3.fa.fai  bowfin-contigs.dot    mpg-6.hist
bowfin-4.dot     bowfin-contigs.fa     mph-6.dist.dot
bowfin-4.fa      bowfin-indel.fa       mph-6.hist
bowfin-4.fa.fai  bowfin-scaffolds.dot  mpi-6.dist.dot
bowfin-4.path1   bowfin-scaffolds.fa   mpi-6.hist
bowfin-4.path2   bowfin-stats          pea-3.dist
bowfin-4.path3   bowfin-stats.csv      pea-3.hist
bowfin-5.dot     bowfin-stats.md       peb-3.dist
bowfin-5.fa      bowfin-stats.tab      peb-3.hist
bowfin-5.path    bowfin-unitigs.fa     slurm.rhea-07.751256.out