cat input.txt

TRINITY_DN106621_c0_g1_i1       TRINITY_DN129833_c0_g1_i2

TRINITY_DN106621_c0_g1_i1       TRINITY_DN140628_c4_g2_i2

TRINITY_DN106621_c0_g1_i1       TRINITY_DN135041_c0_g1_i1

TRINITY_DN135041_c0_g1_i1       TRINITY_DN106621_c0_g1_i1

TRINITY_DN140628_c4_g2_i2       TRINITY_DN106621_c0_g1_i1

TRINITY_DN129833_c0_g1_i2       TRINITY_DN106621_c0_g1_i1

awk '{printf("%s\t%s\n",($1<$2?$1:$2),($1<$2?$2:$1));}' input.txt | sort | uniq > output.txt

cat output.txt

TRINITY_DN106621_c0_g1_i1       TRINITY_DN129833_c0_g1_i2

TRINITY_DN106621_c0_g1_i1       TRINITY_DN140628_c4_g2_i2

TRINITY_DN106621_c0_g1_i1       TRINITY_DN135041_c0_g1_i1