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I'm looking for name of the book about young man flying an interstellar cargo ship alone. His uncle had pre-programmed the ship's computer to ask questions and give directions before dying.

The boy's family had been killed by pirates.

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I came across the book Dragon and Soldier, book two in Timothy Zahn's Dragonback series. This led me to the first book in the series; Dragon and Thief

Jack Morgan is a fourteen-year-old boy, raised by his adoptive uncle, Virgil Morgan, as a professional thief and confidence artist but presently interested in reform. Throughout the first book, he lives aboard the starship Essenay, protected by an artificial intelligence mimicking his uncle.

Virgil Morgan, the adoptive uncle of Jack, is a professional thief and confidence artist, notorious throughout the Orion Arm, and therefore sought as an ally by the story's antagonists; but has died before the events of the initial book, and is represented largely in Jack's memories. Because his death is kept secret by Jack, he is believed alive by supporting characters until the final book.

In the synopsis of the third book (Dragon and Slave), and the fourth book (Dragon and Herdsman), it is mentioned that Jack lost his parents when he was three. Following this link to the Google Books preview of the final book (Dragon and Liberator) has a recording of Uncle Virgil explaining that

Jack's parents were murdered and Uncle Virgil took Jack into his custody. Virgil told Jack his parents died in a mining accident. Virgil's explanation as to how he found the ship is omitted from the preview, but they were killed on the ship and Jack was left alive. Virgil says "A beautiful Judge-Paladin ship, loaded to the intakes with all the finest equipment money can buy" which leads me to believe the ship was attacked by pirates before Virgil came across the ship.

Synopsis of the series:

Jack Morgan is symbiotically linked with a dragon. Belonging to the warrior K’da species of dragons, this type of dragon can only survive six hours without a human host. Jack is chosen by Draycos 30s after he is the only survivor of three ships that have destroyed scouting for refugees, and they combine to make an instant team. Jack is a fourteen year old reformed con man, and now he has a partner in Draycos, who literally lives on his back. Draycos is sentient and two dimensional, while Jack certainly isn’t. Raised by his Uncle Virgil, Jack was taught to follow in his foot steps as a con man and a thief. Before his Uncle Virgil died, he loaded parts of his personality and thoughts into the computer of the ship, and is thus with Jack in some ways.

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Merchanter's Luck by C. J. Cherryh has all the plot elements you mention.

The boy's family had been killed by pirates.

Only three people survive the Mazianni attack on a family merchanter ship: Sandy, the young protagonist, and two of his uncles.

young man flying an interstellar cargo ship alone.

After the two adults are killed (one by a space accident, the other in a fight), Sandy flies the ship alone or with hired help, the former being dangerous and illegal.

His uncle had pre-programmed the ship's computer to ask questions and give directions before dying.

The recorded hints and warnings given by the computer were once essential for Sandy to be able to fly the ship, but at the time of the story, the moral support and psychological relief of hearing the voice of his uncle is more important.

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