We present a new control algorithm and system design for a network of quantum repeaters, and outline the end-to-end protocol architecture. Such a network will create long-distance quantum states, supporting quantum key distribution as well as distributed quantum computation. Quantum repeaters improve the reduction of quantum-communication throughput with distance from exponential to polynomial. Because a quantum state cannot be copied, a quantum repeater is not a signal amplifier. Rather, it executes algorithms for quantum teleportation in conjunction with a specialized type of quantum error correction called purification to raise the fidelity of the quantum states. We introduce our banded purification scheme, which is especially effective when the fidelity of coupled qubits is low, improving the prospects for experimental realization of such systems. The resulting throughput is calculated via detailed simulations of a long line composed of shorter hops. Our algorithmic improvements increase throughput by a factor of up to 50 compared to earlier approaches, for a broad range of physical characteristics.